chr7-105542548-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_021930.6(RINT1):c.414G>A(p.Ala138Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00976 in 1,614,042 control chromosomes in the GnomAD database, including 1,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021930.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0512 AC: 7788AN: 152044Hom.: 700 Cov.: 31
GnomAD3 exomes AF: 0.0136 AC: 3431AN: 251480Hom.: 267 AF XY: 0.00998 AC XY: 1356AN XY: 135916
GnomAD4 exome AF: 0.00543 AC: 7936AN: 1461880Hom.: 601 Cov.: 31 AF XY: 0.00461 AC XY: 3354AN XY: 727246
GnomAD4 genome AF: 0.0514 AC: 7818AN: 152162Hom.: 706 Cov.: 31 AF XY: 0.0511 AC XY: 3804AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:2
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RINT1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at