ENST00000361301.6:c.*113C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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]

ENSG00000308687 (HGNC:):

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361301.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT16	NM_057168.2	MANE Select	c.*113C>T		3_prime_UTR	Exon 4 of 4	NP_476509.1
	WNT16	NM_016087.2		c.*113C>T		3_prime_UTR	Exon 4 of 4	NP_057171.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT16	ENST00000361301.6	TSL:1	c.*113C>T		splice_region	Exon 4 of 4	ENSP00000355065.2
	WNT16	ENST00000222462.3	TSL:1 MANE Select	c.*113C>T		3_prime_UTR	Exon 4 of 4	ENSP00000222462.2
	WNT16	ENST00000361301.6	TSL:1	c.*113C>T		3_prime_UTR	Exon 4 of 4	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

African (AFR) AF: 0.0397 AC: 799 AN: 20128

American (AMR) AF: 0.127 AC: 2775 AN: 21866

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 2097 AN: 16278

East Asian (EAS) AF: 0.000330 AC: 11 AN: 33374

South Asian (SAS) AF: 0.0624 AC: 3511 AN: 56274

European-Finnish (FIN) AF: 0.170 AC: 5208 AN: 30684

Middle Eastern (MID) AF: 0.149 AC: 412 AN: 2764

European-Non Finnish (NFE) AF: 0.156 AC: 93305 AN: 596896

Other (OTH) AF: 0.126 AC: 4803 AN: 38164

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

African (AFR) AF: 0.0535 AC: 1933 AN: 36164

American (AMR) AF: 0.115 AC: 1749 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.0575 AC: 271 AN: 4710

European-Finnish (FIN) AF: 0.161 AC: 1699 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11485 AN: 67984

Other (OTH) AF: 0.124 AC: 257 AN: 2074

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.63
PhyloP100		-0.078
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: rs17143305; hg19: chr7-120979512;