chr7-121337489-T-C

Position:

• chr7-121337489-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000222462.3(WNT16):​c.634-1392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0883 in 152,150 control chromosomes in the GnomAD database, including 941 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 0.088 (941 hom., cov: 32)
• Consequence: WNT16 ENST00000222462.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT16	NM_057168.2	c.634-1392T>C		intron_variant		ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.604-1392T>C		intron_variant			NP_057171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT16	ENST00000222462.3	c.634-1392T>C		intron_variant		1	NM_057168.2	ENSP00000222462	P1
WNT16	ENST00000361301.6	c.604-1392T>C		intron_variant		1		ENSP00000355065

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13437 AN: 152032 Hom.: 940 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.0883 AC: 13440 AN: 152150 Hom.: 941 Cov.: 32 AF XY: 0.0915 AC XY: 6808 AN XY: 74402

Gnomad4 AFR AF: 0.0208

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0961 Hom.: 1090

Bravo AF: 0.0871

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.76

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: rs3801385; hg19: chr7-120977543;