rs34072914

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_003396.3(WNT9B):c.399G>T(p.Arg133Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 1,613,996 control chromosomes in the GnomAD database, including 655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 105 hom., cov: 33)

Exomes 𝑓: 0.025 ( 550 hom. )

Consequence

WNT9B
NM_003396.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.982

Publications

9 publications found

Variant links:

Genes affected

WNT9B (HGNC:12779): (Wnt family member 9B) 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. Study of its expression in the teratocarcinoma cell line NT2 suggests that it may be implicated in the early process of neuronal differentiation of NT2 cells induced by retinoic acid. This gene is clustered with WNT3, another family member, in the chromosome 17q21 region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

WNT9B links:

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRRC37A2 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=-0.5).

BP6

Variant 17-46875165-G-T is Benign according to our data. Variant chr17-46875165-G-T is described in ClinVar as [Benign]. Clinvar id is 1578578.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.982 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.033 (5019/152320) while in subpopulation AFR AF = 0.0487 (2025/41580). AF 95% confidence interval is 0.0469. There are 105 homozygotes in GnomAd4. There are 2326 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 105 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT9B	NM_003396.3 link	c.399G>T	p.Arg133Arg	synonymous_variant	Exon 3 of 4	ENST00000290015.7	NP_003387.1	O14905
WNT9B	NM_001320458.2 link	c.399G>T	p.Arg133Arg	synonymous_variant	Exon 3 of 5		NP_001307387.1	E7EPC3
WNT9B	XM_011525178.3 link	c.417G>T	p.Arg139Arg	synonymous_variant	Exon 3 of 4		XP_011523480.1
LRRC37A2	XM_024450773.2 link	c.4810-173891G>T		intron_variant	Intron 10 of 10		XP_024306541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
WNT9B	ENST00000290015.7 link	c.399G>T	p.Arg133Arg	synonymous_variant	Exon 3 of 4	1	NM_003396.3	ENSP00000290015.2	O14905
WNT9B	ENST00000393461.2 link	c.399G>T	p.Arg133Arg	synonymous_variant	Exon 3 of 5	2		ENSP00000377105.2	E7EPC3
WNT9B	ENST00000575372.5 link	c.*19G>T		downstream_gene_variant		4		ENSP00000458192.1	I3L0L8

Frequencies

GnomAD3 genomes

AF:

0.0329

AC:

5002

AN:

152202

Hom.:

103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0484

Gnomad AMI

AF:

0.0604

Gnomad AMR

AF:

0.0292

Gnomad ASJ

AF:

0.0213

Gnomad EAS

AF:

0.0335

Gnomad SAS

AF:

0.0338

Gnomad FIN

AF:

0.00941

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0279

Gnomad OTH

AF:

0.0310

GnomAD2 exomes

AF:

0.0273

AC:

6838

AN:

250610

AF XY:

0.0276

show subpopulations

Gnomad AFR exome

AF:

0.0493

Gnomad AMR exome

AF:

0.0246

Gnomad ASJ exome

AF:

0.0245

Gnomad EAS exome

AF:

0.0349

Gnomad FIN exome

AF:

0.0100

Gnomad NFE exome

AF:

0.0260

Gnomad OTH exome

AF:

0.0239

GnomAD4 exome

AF:

0.0254

AC:

37058

AN:

1461676

Hom.:

550

Cov.:

AF XY:

0.0258

AC XY:

18782

AN XY:

727162

show subpopulations

African (AFR)

AF:

0.0500

AC:

1674

AN:

33480

American (AMR)

AF:

0.0243

AC:

1086

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0251

AC:

655

AN:

26134

East Asian (EAS)

AF:

0.0325

AC:

1290

AN:

39698

South Asian (SAS)

AF:

0.0328

AC:

2828

AN:

86248

European-Finnish (FIN)

AF:

0.0104

AC:

553

AN:

53230

Middle Eastern (MID)

AF:

0.0355

AC:

205

AN:

5768

European-Non Finnish (NFE)

AF:

0.0244

AC:

27170

AN:

1112000

Other (OTH)

AF:

0.0264

AC:

1597

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

2519

5038

7558

10077

12596

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0330

AC:

5019

AN:

152320

Hom.:

105

Cov.:

AF XY:

0.0312

AC XY:

2326

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0487

AC:

2025

AN:

41580

American (AMR)

AF:

0.0292

AC:

447

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0213

AC:

AN:

3470

East Asian (EAS)

AF:

0.0336

AC:

174

AN:

5178

South Asian (SAS)

AF:

0.0334

AC:

161

AN:

4822

European-Finnish (FIN)

AF:

0.00941

AC:

100

AN:

10626

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0279

AC:

1901

AN:

68028

Other (OTH)

AF:

0.0307

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

261

522

782

1043

1304

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0290

Hom.:

Bravo

AF:

0.0338

Asia WGS

AF:

0.0380

AC:

133

AN:

3478

EpiCase

AF:

0.0295

EpiControl

AF:

0.0274

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 28, 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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.98

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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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rs34072914

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