7-121339471-C-CCTCT

Variant names:

• chr7-121339471-C-CCTCT
• rs3832519
• NM_057168.2:c.*128_*129insCTCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_057168.2(WNT16):​c.*128_*129insCTCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 804,152 control chromosomes in the GnomAD database, including 16,767 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (5944 hom., cov: 25)
  • Exomes 𝑓: 0.17 (10823 hom.)
• Consequence: WNT16 NM_057168.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 7 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_057168.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT16	NM_057168.2	MANE Select	c.*128_*129insCTCT		3_prime_UTR	Exon 4 of 4	NP_476509.1	Q9UBV4-1
	WNT16	NM_016087.2		c.*128_*129insCTCT		3_prime_UTR	Exon 4 of 4	NP_057171.2	Q9UBV4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT16	ENST00000222462.3	TSL:1 MANE Select	c.*128_*129insCTCT		3_prime_UTR	Exon 4 of 4	ENSP00000222462.2	Q9UBV4-1
	ENSG00000308687	ENST00000835700.1		n.188+420_188+421insAGAG		intron	N/A
	WNT16	ENST00000361301.6	TSL:1	c.*126_*127insCTCT		downstream_gene	N/A	ENSP00000355065.2	E9PH60

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37878 AN: 151798 Hom.: 5921 Cov.: 25

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.165 AC: 107694 AN: 652236 Hom.: 10823 Cov.: 9 AF XY: 0.166 AC XY: 55005 AN XY: 332002

African (AFR) AF: 0.443 AC: 6998 AN: 15786

American (AMR) AF: 0.155 AC: 3039 AN: 19616

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 2215 AN: 14984

East Asian (EAS) AF: 0.0285 AC: 923 AN: 32336

South Asian (SAS) AF: 0.193 AC: 9662 AN: 50050

European-Finnish (FIN) AF: 0.179 AC: 5367 AN: 29980

Middle Eastern (MID) AF: 0.195 AC: 468 AN: 2398

European-Non Finnish (NFE) AF: 0.161 AC: 73384 AN: 454398

Other (OTH) AF: 0.172 AC: 5638 AN: 32688

GnomAD4 genome AF: 0.250 AC: 37941 AN: 151916 Hom.: 5944 Cov.: 25 AF XY: 0.246 AC XY: 18241 AN XY: 74268

African (AFR) AF: 0.455 AC: 18782 AN: 41314

American (AMR) AF: 0.165 AC: 2522 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 487 AN: 3464

East Asian (EAS) AF: 0.0430 AC: 223 AN: 5188

South Asian (SAS) AF: 0.206 AC: 994 AN: 4816

European-Finnish (FIN) AF: 0.170 AC: 1802 AN: 10582

Middle Eastern (MID) AF: 0.176 AC: 51 AN: 290

European-Non Finnish (NFE) AF: 0.183 AC: 12456 AN: 67966

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.117 Hom.: 192

Bravo AF: 0.257

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3832519; hg19: chr7-120979525; COSMIC: COSV55975386; COSMIC: COSV55975386;