rs6948009

Variant names:

• chr7-117276359-T-C
• rs6948009
• NM_003391.3:c.*1796A>G

Variant summary

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

The NM_003391.3(WNT2):​c.*1796A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,296 control chromosomes in the GnomAD database, including 1,380 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 0.11 (1380 hom., cov: 33)
• Consequence: WNT2 NM_003391.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT2	NM_003391.3	c.*1796A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000265441.8	NP_003382.1
WNT2	NR_024047.2	n.2884A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT2	ENST00000265441.8	c.*1796A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_003391.3	ENSP00000265441.3
WNT2	ENST00000647844.1	n.*2794A>G		non_coding_transcript_exon_variant	Exon 6 of 6			ENSP00000497695.1
WNT2	ENST00000647844.1	n.*2794A>G		3_prime_UTR_variant	Exon 6 of 6			ENSP00000497695.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16464 AN: 152178 Hom.: 1368 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.108 AC: 16519 AN: 152296 Hom.: 1380 Cov.: 33 AF XY: 0.107 AC XY: 7959 AN XY: 74484

African (AFR) AF: 0.238 AC: 9869 AN: 41530

American (AMR) AF: 0.0713 AC: 1092 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.0202 AC: 105 AN: 5186

South Asian (SAS) AF: 0.0331 AC: 160 AN: 4834

European-Finnish (FIN) AF: 0.0851 AC: 904 AN: 10622

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 3997 AN: 68026

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.0926 Hom.: 119

Bravo AF: 0.112

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.18
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6948009; hg19: chr7-116916413;