rs3209079
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_013382.7(POMT2):c.1911T>G(p.Leu637Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,613,018 control chromosomes in the GnomAD database, including 526,421 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_013382.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.821 AC: 124889AN: 152092Hom.: 51399 Cov.: 33
GnomAD3 exomes AF: 0.815 AC: 203865AN: 250248Hom.: 83457 AF XY: 0.814 AC XY: 110302AN XY: 135472
GnomAD4 exome AF: 0.805 AC: 1176648AN: 1460808Hom.: 474982 Cov.: 72 AF XY: 0.805 AC XY: 584837AN XY: 726742
GnomAD4 genome AF: 0.821 AC: 124983AN: 152210Hom.: 51439 Cov.: 33 AF XY: 0.823 AC XY: 61244AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:5
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Leu637Leu in exon 19 of POMT2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 19.0% (1637/8600) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs3209079). -
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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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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 Benign:1
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Autosomal recessive limb-girdle muscular dystrophy type 2N Benign:1
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not provided Benign:1
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at