rs66502123
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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.334-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,602,448 control chromosomes in the GnomAD database, including 11,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.087 ( 735 hom., cov: 32)
Exomes 𝑓: 0.11 ( 10358 hom. )
Consequence
POMT2
NM_013382.7 intron
NM_013382.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.561
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=-0.71).
BP6
?
Variant 14-77306486-A-G is Benign according to our data. Variant chr14-77306486-A-G is described in ClinVar as [Benign]. Clinvar id is 260300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77306486-A-G is described in Lovd as [Likely_benign]. Variant chr14-77306486-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMT2 | NM_013382.7 | c.334-45T>C | intron_variant | ENST00000261534.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMT2 | ENST00000261534.9 | c.334-45T>C | intron_variant | 1 | NM_013382.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0875 AC: 13310AN: 152158Hom.: 735 Cov.: 32
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GnomAD3 exomes AF: 0.104 AC: 25729AN: 246266Hom.: 1708 AF XY: 0.113 AC XY: 15024AN XY: 133314
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GnomAD4 exome AF: 0.113 AC: 164574AN: 1450172Hom.: 10358 Cov.: 29 AF XY: 0.117 AC XY: 84298AN XY: 721308
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GnomAD4 genome ? AF: 0.0874 AC: 13312AN: 152276Hom.: 735 Cov.: 32 AF XY: 0.0886 AC XY: 6593AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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