3-13854643-A-G

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.459T>C(p.Ser153Ser) 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
NM_004625.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.464

Publications

17 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=-0.8).

BP6

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

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 rank	MANE	Protein	UniProt
WNT7A	NM_004625.4 link	c.459T>C	p.Ser153Ser	synonymous_variant	Exon 3 of 4	ENST00000285018.5	NP_004616.2	O00755
WNT7A	XM_011534091.3 link	c.258T>C	p.Ser86Ser	synonymous_variant	Exon 4 of 5		XP_011532393.1
WNT7A	XM_047448863.1 link	c.258T>C	p.Ser86Ser	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.459T>C	p.Ser153Ser	synonymous_variant	Exon 3 of 4	1	NM_004625.4	ENSP00000285018.4		O00755

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

GnomAD2 exomes

AF:

0.216

AC:

54274

AN:

251326

AF XY:

0.211

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 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

African (AFR)

AF:

0.164

AC:

5478

AN:

33480

American (AMR)

AF:

0.220

AC:

9849

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

3166

AN:

26136

East Asian (EAS)

AF:

0.549

AC:

21776

AN:

39700

South Asian (SAS)

AF:

0.185

AC:

15996

AN:

86258

European-Finnish (FIN)

AF:

0.203

AC:

10838

AN:

53356

Middle Eastern (MID)

AF:

0.150

AC:

866

AN:

5768

European-Non Finnish (NFE)

AF:

0.192

AC:

213849

AN:

1112008

Other (OTH)

AF:

0.199

AC:

11997

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

16738

33477

50215

66954

83692

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7748

15496

23244

30992

38740

<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:

0.194

AC:

29557

AN:

152172

Hom.:

3281

Cov.:

AF XY:

0.196

AC XY:

14606

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.171

AC:

7096

AN:

41516

American (AMR)

AF:

0.192

AC:

2932

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

400

AN:

3468

East Asian (EAS)

AF:

0.560

AC:

2880

AN:

5144

South Asian (SAS)

AF:

0.197

AC:

948

AN:

4816

European-Finnish (FIN)

AF:

0.207

AC:

2194

AN:

10598

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12598

AN:

68008

Other (OTH)

AF:

0.162

AC:

343

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1212

2424

3636

4848

6060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.177

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

- -

Oct 16, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.7

(source)

DANN

Benign

0.56

PhyloP100

-0.46

Mutation Taster

=98/2

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