rs2385199

Positions:

• chr2-218886024-A-G

Variant summary

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

The NM_025216.3(WNT10A):​c.376+3601A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,082 control chromosomes in the GnomAD database, including 5,479 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 0.25 (5479 hom., cov: 32)
• Consequence: WNT10A NM_025216.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

WNT10A (HGNC:13829): (Wnt family member 10A) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is strongly expressed in the cell lines of promyelocytic leukemia and Burkitt's lymphoma. In addition, it and another family member, the WNT6 gene, are strongly coexpressed in colorectal cancer cell lines. The gene overexpression may play key roles in carcinogenesis through activation of the WNT-beta-catenin-TCF signaling pathway. This gene and the WNT6 gene are clustered in the chromosome 2q35 region. [provided by RefSeq, Jul 2008]

WNT10A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT10A	NM_025216.3	c.376+3601A>G		intron_variant		ENST00000258411.8	NP_079492.2
WNT10A	XM_011511929.3	c.280+3601A>G		intron_variant			XP_011510231.1
WNT10A	XM_011511930.2	c.376+3601A>G		intron_variant			XP_011510232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT10A	ENST00000258411.8	c.376+3601A>G		intron_variant		1	NM_025216.3	ENSP00000258411.3
WNT10A	ENST00000458582.1	c.262+3601A>G		intron_variant		3		ENSP00000388812.1
WNT10A	ENST00000483911.1	n.474+1701A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38097 AN: 151964 Hom.: 5467 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.251 AC: 38142 AN: 152082 Hom.: 5479 Cov.: 32 AF XY: 0.249 AC XY: 18530 AN XY: 74360

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.244

Alfa AF: 0.197 Hom.: 3058

Bravo AF: 0.258

Asia WGS AF: 0.325 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.6
DANN	Benign	0.85

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: rs2385199; hg19: chr2-219750746;