chr7-121337489-T-C

Variant names:

• chr7-121337489-T-C
• rs3801385
• NM_057168.2:c.634-1392T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_057168.2(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 NM_057168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 12 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 -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 rank	MANE	Protein	UniProt
WNT16	NM_057168.2	c.634-1392T>C		intron_variant	Intron 3 of 3	ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.604-1392T>C		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.634-1392T>C		intron_variant	Intron 3 of 3	1	NM_057168.2	ENSP00000222462.2
WNT16	ENST00000361301.6	c.604-1392T>C		intron_variant	Intron 3 of 3	1		ENSP00000355065.2

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

African (AFR) AF: 0.0208 AC: 864 AN: 41508

American (AMR) AF: 0.110 AC: 1679 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5168

South Asian (SAS) AF: 0.202 AC: 974 AN: 4826

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0959 AC: 6516 AN: 67972

Other (OTH) AF: 0.0972 AC: 205 AN: 2108

Alfa AF: 0.0942 Hom.: 1314

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
PhyloP100		0.12
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: rs3801385; hg19: chr7-120977543;