Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_006767.4(LZTR1):c.651+10_651+46del

CA249117

218690 (ClinVar)

Gene: LZTR1
Condition: RASopathy
Inheritance Mode: Undetermined mode of inheritance
Link to MONDO
UUID: 47285e4b-40af-4df9-a6a1-4317d2f0d7d6
Approved on: 2024-09-17
Published on: 2024-11-04

HGVS expressions

NM_006767.4:c.651+10_651+46del
NM_006767.4(LZTR1):c.651+10_651+46del
NC_000022.11:g.20989692_20989728del
CM000684.2:g.20989692_20989728del
NC_000022.10:g.21343981_21344017del
CM000684.1:g.21343981_21344017del
NC_000022.9:g.19673981_19674017del
NG_034193.1:g.12424_12460del
ENST00000700578.1:c.651+10_651+46del
ENST00000642151.1:c.482+10_482+46del
ENST00000644435.1:c.473+10_473+46del
ENST00000646124.2:c.651+10_651+46del
ENST00000646506.1:n.230+10_230+46del
ENST00000215739.12:c.651+10_651+46del
ENST00000414985.5:c.*217+10_*217+46del
ENST00000479606.5:n.797+10_797+46del
ENST00000480895.1:n.347+10_347+46del
ENST00000497716.5:n.34+10_34+46del
NM_006767.3:c.651+10_651+46del
More

Likely Benign

Met criteria codes 3
BP7 BP4 BP3
Not Met criteria codes 7
BA1 BS1 PS4 PP3 PM2 PM3 PM4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LZTR1 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The NM_006767.4:c.651+10_651+46del variant is an intronic variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7). The c.651+10_651+46del variant is predicted to cause an in-frame deletion of 37 nucleotides in an intronic repetitive region of no known function, as determined by the ClinGen RASopathy VCEP (BP3). In summary, this variant meets the criteria to be classified as likely benign for RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: BP3, BP4, BP7. (ClinGen RASopathy VCEP specifications version 1.1; 9/17/2024)
Met criteria codes
BP7
The NM_006767.4:c.651+10_651+46del variant is an intronic variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7).
BP4
The NM_006767.4:c.651+10_651+46del variant is an intronic variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7).
BP3
The c.651+10_651+46del variant is predicted to cause an in-frame deletion of 37 nucleotides in an intronic repetitive region of no known function, as determined by the ClinGen RASopathy VCEP (BP3).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The highest population filtering allele frequency in gnomAD v2.1.1 is 0.00002599 (3/30578 alleles) in the South Asian population (PM2_Supporting, BS1, and BA1 are not met).
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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