dbSNP rs9494883: WAKMAR2:n.1056+14830T>C (chr6-137850329-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000606998.2(WAKMAR2):n.1056+14830T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 152,214 control chromosomes in the GnomAD database, including 838 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 0.075 ( 838 hom., cov: 32)

Consequence

WAKMAR2
ENST00000606998.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164

Publications

13 publications found

Variant links:

Genes affected

WAKMAR2 (HGNC:53754): (wound and keratinocyte migration associated lncRNA 2)

WAKMAR2 links:

ENSG00000299400 (HGNC:):

ENSG00000299400 links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1 link	n.1056+14830T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WAKMAR2	ENST00000606998.2 link	n.1056+14830T>C	intron_variant	Intron 3 of 3	2
WAKMAR2	ENST00000763029.1 link	n.592+17313T>C	intron_variant	Intron 1 of 1
WAKMAR2	ENST00000763030.1 link	n.187+5059T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0752

AC:

11433

AN:

152096

Hom.:

837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0420

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.0306

Gnomad SAS

AF:

0.0288

Gnomad FIN

AF:

0.0166

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0290

Gnomad OTH

AF:

0.0612

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

GnomAD4 genome

AF:

0.0753

AC:

11460

AN:

152214

Hom.:

838

Cov.:

AF XY:

0.0736

AC XY:

5481

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.195

AC:

8086

AN:

41486

American (AMR)

AF:

0.0420

AC:

642

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0403

AC:

140

AN:

3470

East Asian (EAS)

AF:

0.0311

AC:

161

AN:

5184

South Asian (SAS)

AF:

0.0286

AC:

138

AN:

4828

European-Finnish (FIN)

AF:

0.0166

AC:

176

AN:

10618

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0290

AC:

1975

AN:

68018

Other (OTH)

AF:

0.0616

AC:

130

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

491

982

1474

1965

2456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0462

Hom.:

375

Bravo

AF:

0.0823

Asia WGS

AF:

0.0400

AC:

142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.67

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over