Variant rs6596422 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001300939.2(WNT8A):c.795G>A(p.Ala265Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,613,938 control chromosomes in the GnomAD database, including 180,986 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 0.44 ( 15206 hom., cov: 32)

Exomes 𝑓: 0.47 ( 165780 hom. )

Consequence

WNT8A
NM_001300939.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.34

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:

WNT8A (HGNC:):

WNT8A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=-2.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT8A	NM_001300939.2 linkuse as main transcript	c.795G>A	p.Ala265Ala	synonymous_variant	5/5	ENST00000506684.6	NP_001287868.1	Q9H1J5D6RF47

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
WNT8A	ENST00000506684.6 linkuse as main transcript	c.795G>A	p.Ala265Ala	synonymous_variant	5/5	1	NM_001300939.2	ENSP00000426653.1	D6RF47
WNT8A	ENST00000504809.5 linkuse as main transcript	c.795G>A	p.Ala265Ala	synonymous_variant	5/6	1		ENSP00000424809.1	D6RF94
WNT8A	ENST00000398754.1 linkuse as main transcript	c.741G>A	p.Ala247Ala	synonymous_variant	6/6	1		ENSP00000381739.1	Q9H1J5-1
WNT8A	ENST00000361560.6 linkuse as main transcript	n.741G>A		non_coding_transcript_exon_variant	6/8	1		ENSP00000354726.2	Q9H1J5-2

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66593

AN:

151958

Hom.:

15205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.604

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.469

GnomAD3 exomes

AF:

0.479

AC:

119406

AN:

249230

Hom.:

29050

AF XY:

0.483

AC XY:

65346

AN XY:

135264

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.439

Gnomad ASJ exome

AF:

0.536

Gnomad EAS exome

AF:

0.589

Gnomad SAS exome

AF:

0.501

Gnomad FIN exome

AF:

0.479

Gnomad NFE exome

AF:

0.482

Gnomad OTH exome

AF:

0.497

GnomAD4 exome

AF:

0.474

AC:

692667

AN:

1461862

Hom.:

165780

Cov.:

AF XY:

0.476

AC XY:

345867

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.335

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.537

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.497

Gnomad4 FIN exome

AF:

0.486

Gnomad4 NFE exome

AF:

0.470

Gnomad4 OTH exome

AF:

0.482

GnomAD4 genome

AF:

0.438

AC:

66621

AN:

152076

Hom.:

15206

Cov.:

AF XY:

0.442

AC XY:

32841

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.457

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.605

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.468

Gnomad4 NFE

AF:

0.471

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.467

Hom.:

11621

Bravo

AF:

0.433

Asia WGS

AF:

0.562

AC:

1958

AN:

3478

EpiCase

AF:

0.489

EpiControl

AF:

0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.44

DANN

Benign

0.55

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over