Variant 1-227924333-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_003395.4(WNT9A):c.420G>A(p.Ala140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.011 in 1,613,620 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0087 ( 11 hom., cov: 32)

Exomes 𝑓: 0.011 ( 125 hom. )

Consequence

WNT9A
NM_003395.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.66

Variant links:

Genes affected

WNT9A (HGNC:12778): (Wnt family member 9A) The WNT gene family consists of structurally related genes that 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 is expressed in gastric cancer cell lines. The protein encoded by this gene shows 75% amino acid identity to chicken Wnt14, which has been shown to play a central role in initiating synovial joint formation in the chick limb. This gene is clustered with another family member, WNT3A, in the chromosome 1q42 region. [provided by RefSeq, Jul 2008]

WNT9A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 1-227924333-C-T is Benign according to our data. Variant chr1-227924333-C-T is described in ClinVar as [Benign]. Clinvar id is 788773.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-5.66 with no splicing effect.

BS2

High AC in GnomAd4 at 1320 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT9A	NM_003395.4 linkuse as main transcript	c.420G>A	p.Ala140=	synonymous_variant	3/4	ENST00000272164.6
WNT9A	XM_011544271.3 linkuse as main transcript	c.210G>A	p.Ala70=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT9A	ENST00000272164.6 linkuse as main transcript	c.420G>A	p.Ala140=	synonymous_variant	3/4	1	NM_003395.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00867

AC:

1320

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00304

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0148

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00517

Gnomad FIN

AF:

0.00169

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0123

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00855

AC:

2143

AN:

250748

Hom.:

AF XY:

0.00887

AC XY:

1203

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.00259

Gnomad AMR exome

AF:

0.00891

Gnomad ASJ exome

AF:

0.00319

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00395

Gnomad FIN exome

AF:

0.00213

Gnomad NFE exome

AF:

0.0135

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.0112

AC:

16427

AN:

1461280

Hom.:

125

Cov.:

AF XY:

0.0111

AC XY:

8088

AN XY:

726994

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00953

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00455

Gnomad4 FIN exome

AF:

0.00215

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.00866

AC:

1320

AN:

152340

Hom.:

Cov.:

AF XY:

0.00844

AC XY:

629

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00303

Gnomad4 AMR

AF:

0.0148

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00518

Gnomad4 FIN

AF:

0.00169

Gnomad4 NFE

AF:

0.0123

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.00962

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0130

EpiControl

AF:

0.0161

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

6.5

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over