14-77288878-T-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013382.7(POMT2):c.1184-47A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,526,204 control chromosomes in the GnomAD database, including 217,298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.51 ( 20408 hom., cov: 29)
Exomes 𝑓: 0.53 ( 196890 hom. )
Consequence
POMT2
NM_013382.7 intron
NM_013382.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.827
Genes affected
POMT2 (HGNC:19743): (protein O-mannosyltransferase 2) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT1 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).[provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 14-77288878-T-G is Benign according to our data. Variant chr14-77288878-T-G is described in ClinVar as [Benign]. Clinvar id is 260290.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77288878-T-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POMT2 | NM_013382.7 | c.1184-47A>C | intron_variant | ENST00000261534.9 | NP_037514.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POMT2 | ENST00000261534.9 | c.1184-47A>C | intron_variant | 1 | NM_013382.7 | ENSP00000261534 | P1 |
Frequencies
GnomAD3 genomes AF: 0.515 AC: 77948AN: 151408Hom.: 20390 Cov.: 29
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GnomAD3 exomes AF: 0.499 AC: 124783AN: 249944Hom.: 32269 AF XY: 0.506 AC XY: 68404AN XY: 135152
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GnomAD4 exome AF: 0.531 AC: 730333AN: 1374678Hom.: 196890 Cov.: 20 AF XY: 0.531 AC XY: 365598AN XY: 689012
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GnomAD4 genome AF: 0.515 AC: 78004AN: 151526Hom.: 20408 Cov.: 29 AF XY: 0.514 AC XY: 38021AN XY: 74024
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | 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. - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2N Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at