NM_001164507.2:c.25564G>A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001164507.2(NEB):c.25564G>A(p.Val8522Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00015 in 1,610,634 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_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.25564G>A | p.Val8522Ile | missense_variant | Exon 182 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.25564G>A | p.Val8522Ile | missense_variant | Exon 182 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000444 AC: 110AN: 247492Hom.: 0 AF XY: 0.000418 AC XY: 56AN XY: 134108
GnomAD4 exome AF: 0.000152 AC: 221AN: 1458334Hom.: 1 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 724762
GnomAD4 genome AF: 0.000138 AC: 21AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74480
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2Benign:1
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. -
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NEB-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at