rs11345097
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001077365.2(POMT1):c.1825+19delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,612,498 control chromosomes in the GnomAD database, including 40 homozygotes. 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POMT1 | NM_001077365.2 | c.1825+19delT | intron_variant | Intron 18 of 19 | ENST00000402686.8 | NP_001070833.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00923 AC: 1403AN: 151958Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.00229 AC: 576AN: 251026Hom.: 10 AF XY: 0.00183 AC XY: 249AN XY: 135738
GnomAD4 exome AF: 0.000869 AC: 1269AN: 1460424Hom.: 14 Cov.: 30 AF XY: 0.000758 AC XY: 551AN XY: 726600
GnomAD4 genome AF: 0.00923 AC: 1403AN: 152074Hom.: 26 Cov.: 32 AF XY: 0.00924 AC XY: 687AN XY: 74360
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at