Variant 3-13854643-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000285018.5(WNT7A):c.459T>C(p.Ser153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,613,998 control chromosomes in the GnomAD database, including 35,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3281 hom., cov: 33)

Exomes 𝑓: 0.20 ( 32519 hom. )

Consequence

WNT7A
ENST00000285018.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.464

Variant links:

Genes affected

WNT7A (HGNC:12786): (Wnt family member 7A) This gene is a member of the WNT gene family, which 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 involved in the development of the anterior-posterior axis in the female reproductive tract, and also plays a critical role in uterine smooth muscle pattering and maintenance of adult uterine function. Mutations in this gene are associated with Fuhrmann and Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndromes. [provided by RefSeq, Jul 2008]

WNT7A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 3-13854643-A-G is Benign according to our data. Variant chr3-13854643-A-G is described in ClinVar as [Benign]. Clinvar id is 1291668.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-13854643-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.464 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
WNT7A	NM_004625.4 linkuse as main transcript	c.459T>C	p.Ser153=	synonymous_variant	3/4	ENST00000285018.5	NP_004616.2
WNT7A	XM_011534091.3 linkuse as main transcript	c.258T>C	p.Ser86=	synonymous_variant	4/5		XP_011532393.1
WNT7A	XM_047448863.1 linkuse as main transcript	c.258T>C	p.Ser86=	synonymous_variant	3/4		XP_047304819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT7A	ENST00000285018.5 linkuse as main transcript	c.459T>C	p.Ser153=	synonymous_variant	3/4	1	NM_004625.4	ENSP00000285018	P1

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29521

AN:

152052

Hom.:

3273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.160

GnomAD3 exomes

AF:

0.216

AC:

54274

AN:

251326

Hom.:

7082

AF XY:

0.211

AC XY:

28665

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.168

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.553

Gnomad SAS exome

AF:

0.187

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.185

Gnomad OTH exome

AF:

0.187

GnomAD4 exome

AF:

0.201

AC:

293815

AN:

1461826

Hom.:

32519

Cov.:

AF XY:

0.200

AC XY:

145307

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.549

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.199

GnomAD4 genome

AF:

0.194

AC:

29557

AN:

152172

Hom.:

3281

Cov.:

AF XY:

0.196

AC XY:

14606

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.185

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.177

Hom.:

1090

Bravo

AF:

0.194

Asia WGS

AF:

0.346

AC:

1202

AN:

3478

EpiCase

AF:

0.178

EpiControl

AF:

0.177

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.7

DANN

Benign

0.56

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