rs4740164
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001077365.2(POMT1):c.913G>A(p.Val305Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0467 in 1,614,046 control chromosomes in the GnomAD database, including 2,249 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001077365.2 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 rank | MANE | Protein | UniProt |
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POMT1 | NM_001077365.2 | c.913G>A | p.Val305Ile | missense_variant | Exon 10 of 20 | ENST00000402686.8 | NP_001070833.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0436 AC: 6632AN: 152166Hom.: 244 Cov.: 33
GnomAD3 exomes AF: 0.0567 AC: 14271AN: 251494Hom.: 634 AF XY: 0.0534 AC XY: 7252AN XY: 135922
GnomAD4 exome AF: 0.0470 AC: 68688AN: 1461762Hom.: 2006 Cov.: 38 AF XY: 0.0462 AC XY: 33562AN XY: 727190
GnomAD4 genome AF: 0.0435 AC: 6627AN: 152284Hom.: 243 Cov.: 33 AF XY: 0.0440 AC XY: 3278AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:8
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
p.Val327Ile in exon 10 of POMT1: This variant is not expected to have clinical s ignificance because it has been identified in 4.6% (399/8600) of European Americ an chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.e du/EVS/; dbSNP rs4740164). -
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Autosomal recessive limb-girdle muscular dystrophy type 2K Benign:2
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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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:2
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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 Benign:1
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Walker-Warburg congenital muscular dystrophy;C1836373:Autosomal recessive limb-girdle muscular dystrophy type 2K;C5436962:Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 Benign:1
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at