dbSNP rs17143305: WNT16:c.*113C>T (chr7-121339458-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780

Publications

11 publications found

Variant links:

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]

WNT16 links:

ENSG00000308687 (HGNC:):

ENSG00000308687 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT16	NM_057168.2 link	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000222462.3	NP_476509.1	Q9UBV4-1
WNT16	NM_016087.2 link	c.*113C>T		3_prime_UTR_variant	Exon 4 of 4		NP_057171.2	Q9UBV4E9PH60

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WNT16	ENST00000361301.6 link	c.*113C>T	splice_region_variant	Exon 4 of 4	1		ENSP00000355065.2	E9PH60
WNT16	ENST00000222462.3 link	c.*113C>T	3_prime_UTR_variant	Exon 4 of 4	1	NM_057168.2	ENSP00000222462.2	Q9UBV4-1
WNT16	ENST00000361301.6 link	c.*113C>T	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000355065.2	E9PH60
ENSG00000308687	ENST00000835700.1 link	n.188+434G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18010

AN:

146492

Hom.:

1341

Cov.:

show subpopulations

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.:

AF XY:

0.136

AC XY:

56050

AN XY:

410998

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

4971

9942

14912

19883

24854

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2402

4804

7206

9608

12010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.123

AC:

18017

AN:

146596

Hom.:

1342

Cov.:

AF XY:

0.120

AC XY:

8606

AN XY:

71618

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11485

AN:

67984

Other (OTH)

AF:

0.124

AC:

257

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

803

1605

2408

3210

4013

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.63

PhyloP100

-0.078

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over