rs537344300
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_015910.7(WDPCP):c.1813-27A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000333 in 1,577,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00034 ( 0 hom. )
Consequence
WDPCP
NM_015910.7 intron
NM_015910.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.55
Genes affected
WDPCP (HGNC:28027): (WD repeat containing planar cell polarity effector) This gene encodes a cytoplasmic WD40 repeat protein. A similar gene in frogs encodes a planar cell polarity protein that plays a critical role in collective cell movement and ciliogenesis by mediating septin localization. Mutations in this gene are associated with Bardet-Biedl syndrome 15 and may also play a role in Meckel-Gruber syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000336 (479/1425108) while in subpopulation AMR AF= 0.00251 (112/44616). AF 95% confidence interval is 0.00213. There are 0 homozygotes in gnomad4_exome. There are 222 alleles in male gnomad4_exome subpopulation. Median coverage is 24. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152166Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000667 AC: 162AN: 243028Hom.: 1 AF XY: 0.000491 AC XY: 65AN XY: 132298
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GnomAD4 exome AF: 0.000336 AC: 479AN: 1425108Hom.: 0 Cov.: 24 AF XY: 0.000312 AC XY: 222AN XY: 711268
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GnomAD4 genome AF: 0.000302 AC: 46AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74460
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 17, 2016 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at