rs142122657
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013382.7(POMT2):c.924-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000497 in 1,610,696 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00029 ( 5 hom. )
Consequence
POMT2
NM_013382.7 splice_polypyrimidine_tract, intron
NM_013382.7 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00001381
2
Clinical Significance
Conservation
PhyloP100: 0.949
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=-0.86).
BP6
?
Variant 14-77298781-G-A is Benign according to our data. Variant chr14-77298781-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 95545.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77298781-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00244 (372/152394) while in subpopulation AFR AF= 0.00827 (344/41594). AF 95% confidence interval is 0.00755. There are 2 homozygotes in gnomad4. There are 187 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMT2 | NM_013382.7 | c.924-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000261534.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMT2 | ENST00000261534.9 | c.924-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_013382.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00244 AC: 372AN: 152276Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000716 AC: 175AN: 244584Hom.: 1 AF XY: 0.000545 AC XY: 72AN XY: 132028
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GnomAD4 exome AF: 0.000293 AC: 428AN: 1458302Hom.: 5 Cov.: 31 AF XY: 0.000263 AC XY: 191AN XY: 725104
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GnomAD4 genome ? AF: 0.00244 AC: 372AN: 152394Hom.: 2 Cov.: 33 AF XY: 0.00251 AC XY: 187AN XY: 74518
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 25, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 17, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 17, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 26, 2017 | 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. - |
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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at