rs3832519

Positions:

• chr7-121339471-C-CCTCT
• chr7-121339471-C-CCTTT

Variant summary

Our verdict is Benign. Variant got -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

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 -8 ACMG points.

• 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/exons	MANE	UniProt
WNT16	NM_057168.2	c.*128_*129insCTCT		3_prime_UTR_variant	4/4	ENST00000222462.3
WNT16	NM_016087.2	c.*128_*129insCTCT		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT16	ENST00000222462.3	c.*128_*129insCTCT		3_prime_UTR_variant	4/4	1	NM_057168.2	P1
WNT16	ENST00000361301.6			downstream_gene_variant		1

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

Gnomad4 AFR exome AF: 0.443

Gnomad4 AMR exome AF: 0.155

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.0285

Gnomad4 SAS exome AF: 0.193

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.172

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

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.228

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3832519; hg19: chr7-120979525;