rs3729629

chr7-117286578-C-Gchr7-117286578-C-T

Variant summary

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

The NM_003391.3(WNT2):c.854-8194G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,980 control chromosomes in the GnomAD database, including 19,277 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 0.50 (19277 hom., cov: 31)
• Consequence: WNT2 NM_003391.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

WNT2 (HGNC:12780): (Wnt family member 2) This gene is a member of the WNT gene family. 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. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT2	NM_003391.3	c.854-8194G>C		intron_variant		ENST00000265441.8
WNT2	NR_024047.2	n.859-8194G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT2	ENST00000265441.8	c.854-8194G>C		intron_variant		1	NM_003391.3	P1
WNT2	ENST00000449446.5	c.*457-8194G>C		intron_variant, NMD_transcript_variant		3
WNT2	ENST00000647844.1	c.*769-8194G>C		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75792 AN: 151860 Hom.: 19262 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.499 AC: 75840 AN: 151980 Hom.: 19277 Cov.: 31 AF XY: 0.501 AC XY: 37180 AN XY: 74282

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.515

Alfa AF: 0.497 Hom.: 2360

Bravo AF: 0.489

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	19
Dann	Benign	0.73

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: rs3729629; hg19: chr7-116926632;