NM_013382.7:c.66C>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_013382.7(POMT2):c.66C>T(p.Gly22Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,589,456 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_013382.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000333 AC: 69AN: 207060Hom.: 0 AF XY: 0.000293 AC XY: 34AN XY: 115922
GnomAD4 exome AF: 0.000117 AC: 168AN: 1437152Hom.: 1 Cov.: 31 AF XY: 0.000108 AC XY: 77AN XY: 714658
GnomAD4 genome AF: 0.000269 AC: 41AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74478
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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not specified Benign:1
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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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POMT2-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at