2-218879152-G-A

Position:

• chr2-218879152-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_011511929.3(WNT10A):​c.18-3009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 150,204 control chromosomes in the GnomAD database, including 8,688 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 0.31 (8688 hom., cov: 27)
• Consequence: WNT10A XM_011511929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

Genes affected

WNT10A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT10A	XM_011511929.3	c.18-3009G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46085 AN: 150090 Hom.: 8674 Cov.: 27

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.307 AC: 46141 AN: 150204 Hom.: 8688 Cov.: 27 AF XY: 0.305 AC XY: 22341 AN XY: 73278

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.295

Alfa AF: 0.224 Hom.: 4478

Bravo AF: 0.323

Asia WGS AF: 0.406 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	21
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806557; hg19: chr2-219743874;