3-13854787-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004625.4(WNT7A):c.315G>A(p.Ala105Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,612,824 control chromosomes in the GnomAD database, including 34,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2711 hom., cov: 33)

Exomes 𝑓: 0.20 ( 31754 hom. )

Consequence

WNT7A
NM_004625.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.591

Publications

19 publications found

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 Gene-Disease associations (from GenCC):

Fuhrmann syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
phocomelia, Schinzel type
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

WNT7A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 3-13854787-C-T is Benign according to our data. Variant chr3-13854787-C-T is described in ClinVar as [Benign]. Clinvar id is 1278485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.591 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 rank	MANE	Protein	UniProt
WNT7A	NM_004625.4 link	c.315G>A	p.Ala105Ala	synonymous_variant	Exon 3 of 4	ENST00000285018.5	NP_004616.2	O00755
WNT7A	XM_011534091.3 link	c.114G>A	p.Ala38Ala	synonymous_variant	Exon 4 of 5		XP_011532393.1
WNT7A	XM_047448863.1 link	c.114G>A	p.Ala38Ala	synonymous_variant	Exon 3 of 4		XP_047304819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT7A	ENST00000285018.5 link	c.315G>A	p.Ala105Ala	synonymous_variant	Exon 3 of 4	1	NM_004625.4	ENSP00000285018.4		O00755

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24672

AN:

152112

Hom.:

2706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0608

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.138

GnomAD2 exomes

AF:

0.208

AC:

51615

AN:

248370

AF XY:

0.205

show subpopulations

Gnomad AFR exome

AF:

0.0580

Gnomad AMR exome

AF:

0.220

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.552

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.183

GnomAD4 exome

AF:

0.197

AC:

288312

AN:

1460594

Hom.:

31754

Cov.:

AF XY:

0.197

AC XY:

142849

AN XY:

726602

show subpopulations

African (AFR)

AF:

0.0542

AC:

1812

AN:

33462

American (AMR)

AF:

0.213

AC:

9522

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

3166

AN:

26136

East Asian (EAS)

AF:

0.548

AC:

21759

AN:

39698

South Asian (SAS)

AF:

0.185

AC:

15972

AN:

86224

European-Finnish (FIN)

AF:

0.203

AC:

10709

AN:

52718

Middle Eastern (MID)

AF:

0.145

AC:

772

AN:

5316

European-Non Finnish (NFE)

AF:

0.192

AC:

213015

AN:

1111996

Other (OTH)

AF:

0.192

AC:

11585

AN:

60324

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

15294

30588

45882

61176

76470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7666

15332

22998

30664

38330

<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:

0.162

AC:

24694

AN:

152230

Hom.:

2711

Cov.:

AF XY:

0.166

AC XY:

12325

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0608

AC:

2526

AN:

41576

American (AMR)

AF:

0.180

AC:

2752

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

400

AN:

3470

East Asian (EAS)

AF:

0.560

AC:

2882

AN:

5146

South Asian (SAS)

AF:

0.197

AC:

949

AN:

4826

European-Finnish (FIN)

AF:

0.207

AC:

2193

AN:

10584

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12534

AN:

68004

Other (OTH)

AF:

0.140

AC:

296

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1037

2074

3111

4148

5185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.173

Hom.:

8840

Bravo

AF:

0.157

Asia WGS

AF:

0.336

AC:

1169

AN:

3478

EpiCase

AF:

0.177

EpiControl

AF:

0.176

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Oct 16, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.67

PhyloP100

-0.59

Mutation Taster

=91/9

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over