rs561658895
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001077365.2(POMT1):c.280+7_280+8del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,608,554 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 3 hom. )
Consequence
POMT1
NM_001077365.2 splice_donor_region, intron
NM_001077365.2 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.126
Genes affected
POMT1 (HGNC:9202): (protein O-mannosyltransferase 1) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT2 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS) and limb-girdle muscular dystrophy type 2K (LGMD2K). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 9-131506458-AAG-A is Benign according to our data. Variant chr9-131506458-AAG-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 436374.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMT1 | NM_001077365.2 | c.280+7_280+8del | splice_donor_region_variant, intron_variant | ENST00000402686.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMT1 | ENST00000402686.8 | c.280+7_280+8del | splice_donor_region_variant, intron_variant | 1 | NM_001077365.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152210Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000489 AC: 123AN: 251472Hom.: 0 AF XY: 0.000589 AC XY: 80AN XY: 135908
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GnomAD4 exome AF: 0.000217 AC: 316AN: 1456226Hom.: 3 AF XY: 0.000295 AC XY: 214AN XY: 724824
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152328Hom.: 2 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74488
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 13, 2016 | - - |
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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at