7-121334711-A-G

Variant names:

• chr7-121334711-A-G
• rs3801387
• NM_057168.2:c.633+2747A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 58 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WNT16	NM_057168.2	c.633+2747A>G		intron_variant	Intron 3 of 3	ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.603+2747A>G		intron_variant	Intron 3 of 3		NP_057171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT16	ENST00000222462.3	c.633+2747A>G		intron_variant	Intron 3 of 3	1	NM_057168.2	ENSP00000222462.2
WNT16	ENST00000361301.6	c.603+2747A>G		intron_variant	Intron 3 of 3	1		ENSP00000355065.2

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

African (AFR) AF: 0.370 AC: 15334 AN: 41442

American (AMR) AF: 0.259 AC: 3960 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3466

East Asian (EAS) AF: 0.126 AC: 655 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4818

European-Finnish (FIN) AF: 0.226 AC: 2383 AN: 10564

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18625 AN: 67876

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.271 Hom.: 18848

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
PhyloP100		4.4
Mutation Taster		=94/6	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: rs3801387; hg19: chr7-120974765;