7-121334711-A-G

Position:

• chr7-121334711-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_057168.2(WNT16):​c.633+2747A>G variant causes a intron change. The variant allele was found at a frequency of 0.289 in 151,950 control chromosomes in the GnomAD database, including 6,673 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 0.29 (6673 hom., cov: 32)
• Consequence: WNT16 NM_057168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.42

Genes affected

WNT16 (HGNC:16267): (Wnt family member 16) 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. This gene is a member of the WNT gene family. It contains two transcript variants diverging at the 5' termini. These two variants are proposed to be the products of separate promoters and not to be splice variants from a single promoter. They are differentially expressed in normal tissues, one of which (variant 2) is expressed at significant levels only in the pancreas, whereas another one (variant 1) is expressed more ubiquitously with highest levels in adult kidney, placenta, brain, heart, and spleen. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT16	NM_057168.2	c.633+2747A>G		intron_variant		ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.603+2747A>G		intron_variant			NP_057171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT16	ENST00000222462.3	c.633+2747A>G		intron_variant		1	NM_057168.2	ENSP00000222462	P1
WNT16	ENST00000361301.6	c.603+2747A>G		intron_variant		1		ENSP00000355065

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43940 AN: 151832 Hom.: 6662 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.289 AC: 43970 AN: 151950 Hom.: 6673 Cov.: 32 AF XY: 0.282 AC XY: 20933 AN XY: 74276

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.291

Alfa AF: 0.261 Hom.: 6149

Bravo AF: 0.298

Asia WGS AF: 0.222 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.78

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: rs3801387; hg19: chr7-120974765;