chr7-121339471-C-CCTAT

Variant names:

• chr7-121339471-C-CCTAT
• rs3832519
• NM_057168.2:c.*128_*129insATCT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_057168.2(WNT16):​c.*128_*129insATCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000153 in 653,046 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: WNT16 NM_057168.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 0.00000153 AC: 1 AN: 653046 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 332438

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 15800

American (AMR) AF: 0.00 AC: 0 AN: 19618

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14990

East Asian (EAS) AF: 0.00 AC: 0 AN: 32336

South Asian (SAS) AF: 0.00 AC: 0 AN: 50084

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29988

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2400

European-Non Finnish (NFE) AF: 0.00000220 AC: 1 AN: 455102

Other (OTH) AF: 0.00 AC: 0 AN: 32728

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.21

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;