7-117280916-T-C

Position:

• chr7-117280916-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.854-2532A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,528 control chromosomes in the GnomAD database, including 30,478 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 0.63 (30478 hom., cov: 32)
• Consequence: WNT2 NM_003391.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT2	NM_003391.3	c.854-2532A>G		intron_variant		ENST00000265441.8	NP_003382.1
WNT2	NR_024047.2	n.859-2532A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT2	ENST00000265441.8	c.854-2532A>G		intron_variant		1	NM_003391.3	ENSP00000265441	P1
WNT2	ENST00000449446.5	c.*457-2532A>G		intron_variant, NMD_transcript_variant		3		ENSP00000389643
WNT2	ENST00000647844.1	c.*769-2532A>G		intron_variant, NMD_transcript_variant				ENSP00000497695

Frequencies

GnomAD3 genomes AF: 0.633 AC: 95813 AN: 151410 Hom.: 30445 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.633 AC: 95888 AN: 151528 Hom.: 30478 Cov.: 32 AF XY: 0.637 AC XY: 47140 AN XY: 73996

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.638

Alfa AF: 0.599 Hom.: 27587

Bravo AF: 0.642

Asia WGS AF: 0.711 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.62

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: rs916725; hg19: chr7-116920970;