rs733154

Variant names:

• chr7-117278857-A-G
• rs733154
• NM_003391.3:c.854-473T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-117278857-A-G
• chr7-117278857-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003391.3(WNT2):​c.854-473T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,014 control chromosomes in the GnomAD database, including 16,516 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 0.46 (16516 hom., cov: 32)
• Consequence: WNT2 NM_003391.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003391.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT2	NM_003391.3	MANE Select	c.854-473T>C		intron	N/A	NP_003382.1
	WNT2	NR_024047.2		n.859-473T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT2	ENST00000265441.8	TSL:1 MANE Select	c.854-473T>C		intron	N/A	ENSP00000265441.3
	WNT2	ENST00000449446.5	TSL:3	n.*457-473T>C		intron	N/A	ENSP00000389643.1
	WNT2	ENST00000647844.1		n.*769-473T>C		intron	N/A	ENSP00000497695.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70174 AN: 151896 Hom.: 16522 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.462 AC: 70179 AN: 152014 Hom.: 16516 Cov.: 32 AF XY: 0.462 AC XY: 34337 AN XY: 74292

African (AFR) AF: 0.425 AC: 17636 AN: 41462

American (AMR) AF: 0.435 AC: 6642 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1759 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5168

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5852 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33751 AN: 67966

Other (OTH) AF: 0.490 AC: 1033 AN: 2110

Alfa AF: 0.482 Hom.: 3603

Bravo AF: 0.453

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		-0.020
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs733154; hg19: chr7-116918911;