rs13431765

Variant names:

• chr2-63190594-T-G
• rs13431765
• NM_015910.7:c.1916-15762A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015910.7(WDPCP):​c.1916-15762A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,042 control chromosomes in the GnomAD database, including 2,569 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2569 hom., cov: 31)
• Consequence: WDPCP NM_015910.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 5 publications found

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]

WDPCP Gene-Disease associations (from GenCC):

• Bardet-Biedl syndrome 15

  Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• Bardet-Biedl syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• heart defect - tongue hamartoma - polysyndactyly syndrome

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000286480 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDPCP	NM_015910.7	c.1916-15762A>C		intron_variant	Intron 14 of 17	ENST00000272321.12	NP_056994.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDPCP	ENST00000272321.12	c.1916-15762A>C		intron_variant	Intron 14 of 17	1	NM_015910.7	ENSP00000272321.7

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26735 AN: 151926 Hom.: 2570 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.176 AC: 26738 AN: 152042 Hom.: 2569 Cov.: 31 AF XY: 0.173 AC XY: 12878 AN XY: 74312

African (AFR) AF: 0.131 AC: 5440 AN: 41490

American (AMR) AF: 0.150 AC: 2295 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3466

East Asian (EAS) AF: 0.0466 AC: 242 AN: 5188

South Asian (SAS) AF: 0.143 AC: 686 AN: 4808

European-Finnish (FIN) AF: 0.172 AC: 1808 AN: 10536

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14992 AN: 67968

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.208 Hom.: 2707

Bravo AF: 0.174

Asia WGS AF: 0.103 AC: 356 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.2
DANN	Benign	0.58
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13431765; hg19: chr2-63417729;