rs7153929
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013382.7(POMT2):c.1117-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 578,046 control chromosomes in the GnomAD database, including 3,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_013382.7 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.113 AC: 13059AN: 115916Hom.: 1264 Cov.: 21
GnomAD3 exomes AF: 0.0648 AC: 11401AN: 175986Hom.: 823 AF XY: 0.0614 AC XY: 5894AN XY: 96020
GnomAD4 exome AF: 0.115 AC: 53027AN: 462044Hom.: 2087 Cov.: 9 AF XY: 0.109 AC XY: 26728AN XY: 245522
GnomAD4 genome AF: 0.113 AC: 13078AN: 116002Hom.: 1264 Cov.: 21 AF XY: 0.115 AC XY: 6145AN XY: 53358
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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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2;C3150416:Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2;C3150418:Autosomal recessive limb-girdle muscular dystrophy type 2N Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at