rs10187013

Positions:

• chr2-63831685-A-G

Variant summary

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

The XM_047444626.1(WDPCP):​c.-4903+8358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 148,922 control chromosomes in the GnomAD database, including 5,003 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 0.22 (5003 hom., cov: 32)
• Consequence: WDPCP XM_047444626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

WDPCP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDPCP	XM_047444626.1	c.-4903+8358T>C		intron_variant			XP_047300582.1
WDPCP	XM_047444627.1	c.-516+8358T>C		intron_variant			XP_047300583.1
WDPCP	XM_047444629.1	c.-430+8358T>C		intron_variant			XP_047300585.1
WDPCP	XM_047444631.1	c.-430+8358T>C		intron_variant			XP_047300587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33418 AN: 148858 Hom.: 5003 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.225 AC: 33441 AN: 148922 Hom.: 5003 Cov.: 32 AF XY: 0.231 AC XY: 16737 AN XY: 72606

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.235

Alfa AF: 0.217 Hom.: 2366

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10187013; hg19: chr2-64058819; COSMIC: COSV71962424;