dbSNP rs1530364: WNT9B:c.335-690G>A (chr17-46874411-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003396.3(WNT9B):c.335-690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,042 control chromosomes in the GnomAD database, including 6,770 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 6770 hom., cov: 32)

Consequence

WNT9B
NM_003396.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

Publications

13 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003396.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT9B	NM_003396.3	MANE Select	c.335-690G>A		intron	N/A	NP_003387.1	O14905
	WNT9B	NM_001320458.2		c.335-690G>A		intron	N/A	NP_001307387.1	E7EPC3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
WNT9B	ENST00000290015.7	TSL:1 MANE Select	c.335-690G>A	intron	N/A	ENSP00000290015.2	O14905
WNT9B	ENST00000393461.2	TSL:2	c.335-690G>A	intron	N/A	ENSP00000377105.2	E7EPC3
WNT9B	ENST00000575372.5	TSL:4	c.353-690G>A	intron	N/A	ENSP00000458192.1	I3L0L8

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

44895

AN:

151924

Hom.:

6759

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.295

AC:

44927

AN:

152042

Hom.:

6770

Cov.:

AF XY:

0.298

AC XY:

22148

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.276

AC:

11438

AN:

41458

American (AMR)

AF:

0.342

AC:

5230

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

972

AN:

3470

East Asian (EAS)

AF:

0.298

AC:

1540

AN:

5174

South Asian (SAS)

AF:

0.324

AC:

1562

AN:

4814

European-Finnish (FIN)

AF:

0.318

AC:

3353

AN:

10556

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19768

AN:

67958

Other (OTH)

AF:

0.310

AC:

655

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1610

3220

4830

6440

8050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.294

Hom.:

5145

Bravo

AF:

0.296

Asia WGS

AF:

0.303

AC:

1050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.93

(source)

DANN

Benign

0.43

PhyloP100

-0.21

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over