rs59515295
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001077365.2(POMT1):c.1082+16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,612,492 control chromosomes in the GnomAD database, including 15,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001077365.2 intron
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 |
---|---|---|---|---|---|---|---|---|
POMT1 | NM_001077365.2 | c.1082+16G>A | intron_variant | Intron 11 of 19 | ENST00000402686.8 | NP_001070833.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.138 AC: 21050AN: 152006Hom.: 1610 Cov.: 31
GnomAD3 exomes AF: 0.116 AC: 28784AN: 248402Hom.: 2012 AF XY: 0.113 AC XY: 15229AN XY: 134290
GnomAD4 exome AF: 0.131 AC: 191590AN: 1460368Hom.: 13692 Cov.: 36 AF XY: 0.129 AC XY: 93525AN XY: 726334
GnomAD4 genome AF: 0.138 AC: 21062AN: 152124Hom.: 1611 Cov.: 31 AF XY: 0.139 AC XY: 10359AN XY: 74396
ClinVar
Submissions by phenotype
not specified Benign:6
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Autosomal recessive limb-girdle muscular dystrophy type 2K Benign:1
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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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not provided 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