rs113174390
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001164507.2(NEB):c.4198G>A(p.Ala1400Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.4198G>A | p.Ala1400Thr | missense_variant | 37/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.4198G>A | p.Ala1400Thr | missense_variant | 37/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.4198G>A | p.Ala1400Thr | missense_variant | 37/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.4198G>A | p.Ala1400Thr | missense_variant | 37/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.4198G>A | p.Ala1400Thr | missense_variant | 37/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000189 AC: 47AN: 249228Hom.: 0 AF XY: 0.000200 AC XY: 27AN XY: 135200
GnomAD4 exome AF: 0.000109 AC: 160AN: 1461680Hom.: 0 Cov.: 31 AF XY: 0.000122 AC XY: 89AN XY: 727122
GnomAD4 genome AF: 0.000473 AC: 72AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74472
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 23, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2013 | This alteration is classified as likely benign based on a combination of the following: 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at