rs6948009

chr7-117276359-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
WNT2	NM_003391.3	c.*1796A>G		3_prime_UTR_variant	5/5	ENST00000265441.8
WNT2	NR_024047.2	n.2884A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT2	ENST00000265441.8	c.*1796A>G		3_prime_UTR_variant	5/5	1	NM_003391.3	P1
WNT2	ENST00000647844.1	c.*2794A>G		3_prime_UTR_variant, NMD_transcript_variant	6/6

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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.0202

Gnomad4 SAS AF: 0.0331

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.0588

Gnomad4 OTH AF: 0.102

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6948009; hg19: chr7-116916413;