7-117277373-G-A

Variant names:

• chr7-117277373-G-A
• rs2024233
• NM_003391.3:c.*782C>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.*782C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,038 control chromosomes in the GnomAD database, including 34,658 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 0.67 (34654 hom., cov: 32)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: WNT2 NM_003391.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440
• Publications: 19 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT2	NM_003391.3	c.*782C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000265441.8	NP_003382.1
WNT2	NR_024047.2	n.1870C>T		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.*782C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_003391.3	ENSP00000265441.3
WNT2	ENST00000647844.1	n.*1780C>T		non_coding_transcript_exon_variant	Exon 6 of 6			ENSP00000497695.1
WNT2	ENST00000647844.1	n.*1780C>T		3_prime_UTR_variant	Exon 6 of 6			ENSP00000497695.1
WNT2	ENST00000449446.5	n.*1468C>T		downstream_gene_variant		3		ENSP00000389643.1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102206 AN: 151912 Hom.: 34628 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.704

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 8 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.673 AC: 102281 AN: 152030 Hom.: 34654 Cov.: 32 AF XY: 0.673 AC XY: 50000 AN XY: 74318

African (AFR) AF: 0.682 AC: 28268 AN: 41460

American (AMR) AF: 0.703 AC: 10740 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2335 AN: 3464

East Asian (EAS) AF: 0.530 AC: 2734 AN: 5160

South Asian (SAS) AF: 0.550 AC: 2642 AN: 4808

European-Finnish (FIN) AF: 0.723 AC: 7640 AN: 10574

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45614 AN: 67962

Other (OTH) AF: 0.704 AC: 1489 AN: 2116

Alfa AF: 0.670 Hom.: 40004

Bravo AF: 0.672

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.32
PhyloP100		0.44
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: rs2024233; hg19: chr7-116917427;