11-118349027-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS1
The NM_000073.3(CD3G):c.56G>A(p.Gly19Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,614,066 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000073.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD3G | NM_000073.3 | c.56G>A | p.Gly19Asp | missense_variant, splice_region_variant | 2/7 | ENST00000532917.3 | |
CD3G | XM_005271724.5 | c.56G>A | p.Gly19Asp | missense_variant, splice_region_variant | 2/4 | ||
CD3G | XM_006718941.4 | c.56G>A | p.Gly19Asp | missense_variant, splice_region_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD3G | ENST00000532917.3 | c.56G>A | p.Gly19Asp | missense_variant, splice_region_variant | 2/7 | 1 | NM_000073.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000697 AC: 106AN: 152144Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000744 AC: 187AN: 251428Hom.: 0 AF XY: 0.000765 AC XY: 104AN XY: 135878
GnomAD4 exome AF: 0.00123 AC: 1793AN: 1461804Hom.: 1 Cov.: 32 AF XY: 0.00117 AC XY: 849AN XY: 727202
GnomAD4 genome AF: 0.000696 AC: 106AN: 152262Hom.: 1 Cov.: 32 AF XY: 0.000578 AC XY: 43AN XY: 74440
ClinVar
Submissions by phenotype
Combined immunodeficiency due to CD3gamma deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2019 | - - |
CD3G-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 29, 2023 | This variant is classified as likely 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