rs2138798

Positions:

• chr2-63284300-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015910.7(WDPCP):​c.1813-24891C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,036 control chromosomes in the GnomAD database, including 3,785 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 0.20 (3785 hom., cov: 32)
• Consequence: WDPCP NM_015910.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDPCP	NM_015910.7	c.1813-24891C>A		intron_variant		ENST00000272321.12	NP_056994.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDPCP	ENST00000272321.12	c.1813-24891C>A		intron_variant		1	NM_015910.7	ENSP00000272321	P1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30144 AN: 151918 Hom.: 3781 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.198 AC: 30175 AN: 152036 Hom.: 3785 Cov.: 32 AF XY: 0.201 AC XY: 14965 AN XY: 74310

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.199

Alfa AF: 0.156 Hom.: 1615

Bravo AF: 0.203

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs2138798; hg19: chr2-63511435;