dbSNP rs2040862: WNT8A:c.156+17C>T (chr5-138084300-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 NM_001300939.2(WNT8A):c.156+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,613,146 control chromosomes in the GnomAD database, including 22,020 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1572 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20448 hom. )

Consequence

WNT8A
NM_001300939.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129

Publications

47 publications found

Variant links:

Genes affected

WNT8A (HGNC:12788): (Wnt family member 8A) 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, and may be implicated in development of early embryos as well as germ cell tumors. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2014]

WNT8A 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT8A	NM_001300939.2 link	c.156+17C>T		intron_variant	Intron 1 of 4	ENST00000506684.6	NP_001287868.1	Q9H1J5D6RF47

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WNT8A	ENST00000506684.6 link	c.156+17C>T	intron_variant	Intron 1 of 4	1	NM_001300939.2	ENSP00000426653.1	D6RF47
WNT8A	ENST00000504809.5 link	c.156+17C>T	intron_variant	Intron 1 of 5	1		ENSP00000424809.1	D6RF94
WNT8A	ENST00000398754.1 link	c.102+17C>T	intron_variant	Intron 2 of 5	1		ENSP00000381739.1	Q9H1J5-1
WNT8A	ENST00000361560.6 link	n.102+17C>T	intron_variant	Intron 2 of 7	1		ENSP00000354726.2	Q9H1J5-2

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20009

AN:

151982

Hom.:

1572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0680

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.0733

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.126

GnomAD2 exomes

AF:

0.131

AC:

32523

AN:

248860

AF XY:

0.131

show subpopulations

Gnomad AFR exome

AF:

0.0694

Gnomad AMR exome

AF:

0.0726

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.134

GnomAD4 exome

AF:

0.160

AC:

234338

AN:

1461046

Hom.:

20448

Cov.:

AF XY:

0.158

AC XY:

115095

AN XY:

726764

show subpopulations

African (AFR)

AF:

0.0663

AC:

2219

AN:

33458

American (AMR)

AF:

0.0750

AC:

3353

AN:

44692

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

4225

AN:

26106

East Asian (EAS)

AF:

0.00106

AC:

AN:

39694

South Asian (SAS)

AF:

0.0776

AC:

6688

AN:

86188

European-Finnish (FIN)

AF:

0.208

AC:

11083

AN:

53352

Middle Eastern (MID)

AF:

0.0836

AC:

482

AN:

5766

European-Non Finnish (NFE)

AF:

0.178

AC:

197630

AN:

1111422

Other (OTH)

AF:

0.143

AC:

8616

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

9735

19471

29206

38942

48677

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6776

13552

20328

27104

33880

<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:

0.132

AC:

20010

AN:

152100

Hom.:

1572

Cov.:

AF XY:

0.132

AC XY:

9819

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0679

AC:

2817

AN:

41496

American (AMR)

AF:

0.108

AC:

1643

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

565

AN:

3470

East Asian (EAS)

AF:

0.00270

AC:

AN:

5180

South Asian (SAS)

AF:

0.0728

AC:

351

AN:

4824

European-Finnish (FIN)

AF:

0.222

AC:

2348

AN:

10558

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11912

AN:

67976

Other (OTH)

AF:

0.125

AC:

263

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

855

1710

2566

3421

4276

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.154

Hom.:

8596

Bravo

AF:

0.120

Asia WGS

AF:

0.0410

AC:

144

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.7

(source)

DANN

Benign

0.49

PhyloP100

0.13

PromoterAI

0.035

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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