rs262489

Variant names:

• chr2-63609133-G-A
• rs262489
• ENST00000467687.1:n.488+41526C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-63609133-G-A
• chr2-63609133-G-C
• chr2-63609133-G-T

Variant summary

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

The ENST00000467687.1(WDPCP):​n.488+41526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,070 control chromosomes in the GnomAD database, including 49,664 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 0.80 (49664 hom., cov: 31)
• Consequence: WDPCP ENST00000467687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 2 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDPCP	XM_047444626.1	c.-249-37507C>T		intron_variant	Intron 4 of 20		XP_047300582.1
WDPCP	XM_047444627.1	c.-249-37507C>T		intron_variant	Intron 3 of 19		XP_047300583.1
WDPCP	XM_047444628.1	c.-249-37507C>T		intron_variant	Intron 2 of 18		XP_047300584.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDPCP	ENST00000467687.1	n.488+41526C>T		intron_variant	Intron 3 of 4	5
WDPCP	ENST00000490935.5	n.583+41526C>T		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121945 AN: 151952 Hom.: 49594 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.803 AC: 122079 AN: 152070 Hom.: 49664 Cov.: 31 AF XY: 0.806 AC XY: 59933 AN XY: 74328

African (AFR) AF: 0.922 AC: 38266 AN: 41514

American (AMR) AF: 0.824 AC: 12582 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2757 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5067 AN: 5162

South Asian (SAS) AF: 0.832 AC: 4011 AN: 4822

European-Finnish (FIN) AF: 0.780 AC: 8235 AN: 10560

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48545 AN: 67948

Other (OTH) AF: 0.770 AC: 1626 AN: 2112

Alfa AF: 0.752 Hom.: 5628

Bravo AF: 0.810

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.81
DANN	Benign	0.65
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs262489; hg19: chr2-63836267;