NM_018972.4:c.965C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_018972.4(GDAP1):c.965C>T(p.Thr322Met) variant causes a missense change. The variant allele was found at a frequency of 0.000177 in 1,614,016 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018972.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000298 AC: 75AN: 251414Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135884
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461866Hom.: 1 Cov.: 32 AF XY: 0.000180 AC XY: 131AN XY: 727228
GnomAD4 genome AF: 0.000125 AC: 19AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
This variant is associated with the following publications: (PMID: 25614874) -
BS1 -
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Charcot-Marie-Tooth disease Uncertain:1
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Charcot-Marie-Tooth disease recessive intermediate A Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Charcot-Marie-Tooth disease, axonal, with vocal cord paresis, autosomal recessive Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
Charcot-Marie-Tooth disease type 4A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at