9-131510049-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_007171.4(POMT1):āc.752A>Gā(p.Gln251Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 1,614,106 control chromosomes in the GnomAD database, including 714,950 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q251W) has been classified as Likely benign.
Frequency
Consequence
NM_007171.4 missense
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.699+53A>G | intron_variant | Intron 8 of 19 | ENST00000402686.8 | NP_001070833.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.887 AC: 134972AN: 152110Hom.: 60591 Cov.: 33
GnomAD3 exomes AF: 0.924 AC: 231971AN: 251126Hom.: 107708 AF XY: 0.932 AC XY: 126534AN XY: 135722
GnomAD4 exome AF: 0.945 AC: 1381729AN: 1461878Hom.: 654330 Cov.: 83 AF XY: 0.947 AC XY: 688666AN XY: 727236
GnomAD4 genome AF: 0.887 AC: 135043AN: 152228Hom.: 60620 Cov.: 33 AF XY: 0.889 AC XY: 66184AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 11, 2014 | This is a RefSeq error. The reference base (c.752A) is the minor allele. This al lele (A) has been identified in 5% (417/8600) of European American chromosomes a nd 26% (1153/4406) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs2296949). - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2K Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at