chr3-142558733-A-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001184.4(ATR):c.1776T>A(p.Gly592Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,609,390 control chromosomes in the GnomAD database, including 272,130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001184.4 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: 0.626 AC: 95066AN: 151788Hom.: 30738 Cov.: 31
GnomAD3 exomes AF: 0.546 AC: 136880AN: 250500Hom.: 38556 AF XY: 0.542 AC XY: 73359AN XY: 135456
GnomAD4 exome AF: 0.572 AC: 833137AN: 1457486Hom.: 241341 Cov.: 36 AF XY: 0.567 AC XY: 411520AN XY: 725186
GnomAD4 genome AF: 0.626 AC: 95163AN: 151904Hom.: 30789 Cov.: 31 AF XY: 0.618 AC XY: 45910AN XY: 74236
ClinVar
Submissions by phenotype
not specified Benign:5
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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 -
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not provided Benign:4
Variant summary: The c.1776T>A variant involves the alteration of a non-conserved nucleotide resulting in a synonymous change. 4/4 in silico tools via Alamut predict the variant to eliminate a cryptic splice donor site, thereby potential resulting in a protective effect on normal splicing. The variant was observed in the large, broad control population, ExAC, with an allele frequency of 55% which includes 19,239 homozygous occurrences. Therefore this synonymous variant is the major allele and has been classified as Benign. -
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Seckel syndrome 1 Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at