rs2707469

Variant names:

• chr7-121336832-A-G
• rs2707469
• NM_057168.2:c.634-2049A>G

Variant summary

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

The NM_057168.2(WNT16):​c.634-2049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,888 control chromosomes in the GnomAD database, including 5,918 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 0.25 (5918 hom., cov: 32)
• Consequence: WNT16 NM_057168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT16	NM_057168.2	c.634-2049A>G		intron_variant	Intron 3 of 3	ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.604-2049A>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.634-2049A>G		intron_variant	Intron 3 of 3	1	NM_057168.2	ENSP00000222462.2
WNT16	ENST00000361301.6	c.604-2049A>G		intron_variant	Intron 3 of 3	1		ENSP00000355065.2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37839 AN: 151768 Hom.: 5894 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.250 AC: 37904 AN: 151888 Hom.: 5918 Cov.: 32 AF XY: 0.245 AC XY: 18223 AN XY: 74258

African (AFR) AF: 0.454 AC: 18766 AN: 41320

American (AMR) AF: 0.165 AC: 2520 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.0432 AC: 224 AN: 5190

South Asian (SAS) AF: 0.206 AC: 993 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12442 AN: 67936

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.287 Hom.: 2823

Bravo AF: 0.257

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.68
PhyloP100		0.47
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: rs2707469; hg19: chr7-120976886;