rs17143305

Variant names:

• chr7-121339458-C-T
• rs17143305
• ENST00000361301.6:c.*113C>T

Variant summary

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

The ENST00000361301.6(WNT16):​c.*113C>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 963,024 control chromosomes in the GnomAD database, including 10,590 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1342 hom., cov: 32)
  • Exomes 𝑓: 0.14 (9248 hom.)
• Consequence: WNT16 ENST00000361301.6 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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 (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT16	NM_057168.2	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000222462.3	NP_476509.1
WNT16	NM_016087.2	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4		NP_057171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT16	ENST00000361301.6	c.*113C>T		splice_region_variant	Exon 4 of 4	1		ENSP00000355065.2
WNT16	ENST00000222462.3	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_057168.2	ENSP00000222462.2
WNT16	ENST00000361301.6	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000355065.2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18010 AN: 146492 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.138 AC: 112921 AN: 816428 Hom.: 9248 Cov.: 11 AF XY: 0.136 AC XY: 56050 AN XY: 410998

Gnomad4 AFR exome AF: 0.0397

Gnomad4 AMR exome AF: 0.127

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.000330

Gnomad4 SAS exome AF: 0.0624

Gnomad4 FIN exome AF: 0.170

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.123 AC: 18017 AN: 146596 Hom.: 1342 Cov.: 32 AF XY: 0.120 AC XY: 8606 AN XY: 71618

Gnomad4 AFR AF: 0.0535

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0575

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.124

Alfa AF: 0.160 Hom.: 446

Bravo AF: 0.112

Asia WGS AF: 0.0390 AC: 135 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	6.1
DANN	Benign	0.63

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: rs17143305; hg19: chr7-120979512;