chr5-151253271-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000405.5(GM2A):c.55G>A(p.Ala19Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 1,613,552 control chromosomes in the GnomAD database, including 2,409 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A19A) has been classified as Likely benign.
Frequency
Consequence
NM_000405.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GM2A | NM_000405.5 | c.55G>A | p.Ala19Thr | missense_variant | 1/4 | ENST00000357164.4 | |
GM2A | NM_001167607.3 | c.55G>A | p.Ala19Thr | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GM2A | ENST00000357164.4 | c.55G>A | p.Ala19Thr | missense_variant | 1/4 | 1 | NM_000405.5 | P1 | |
GM2A | ENST00000523466.5 | c.127-6484G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0399 AC: 6070AN: 152152Hom.: 263 Cov.: 32
GnomAD3 exomes AF: 0.0607 AC: 15228AN: 251070Hom.: 810 AF XY: 0.0591 AC XY: 8029AN XY: 135744
GnomAD4 exome AF: 0.0402 AC: 58768AN: 1461282Hom.: 2148 Cov.: 31 AF XY: 0.0408 AC XY: 29644AN XY: 727032
GnomAD4 genome AF: 0.0398 AC: 6065AN: 152270Hom.: 261 Cov.: 32 AF XY: 0.0425 AC XY: 3162AN XY: 74454
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 03, 2015 | - - |
Tay-Sachs disease, variant AB Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, 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 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. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 15, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at