dbSNP rs59693083: WAKMAR2:n.160T>C (chr6-137865395-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 ENST00000763036.1(WAKMAR2):n.160T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,420 control chromosomes in the GnomAD database, including 5,019 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 0.19 ( 5019 hom., cov: 32)

Exomes 𝑓: 0.066 ( 0 hom. )

Consequence

WAKMAR2
ENST00000763036.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Publications

9 publications found

Variant links:

Genes affected

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

WAKMAR2 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1 link	n.895-75T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
WAKMAR2	ENST00000763036.1 link	n.160T>C	non_coding_transcript_exon_variant	Exon 1 of 3
WAKMAR2	ENST00000763056.1 link	n.1576T>C	non_coding_transcript_exon_variant	Exon 2 of 2
WAKMAR2	ENST00000763058.1 link	n.1641T>C	non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29066

AN:

152072

Hom.:

4998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0559

Gnomad SAS

AF:

0.0976

Gnomad FIN

AF:

0.0254

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0801

Gnomad OTH

AF:

0.175

GnomAD4 exome

AF:

0.0658

AC:

AN:

228

Hom.:

AF XY:

0.0429

AC XY:

AN XY:

140

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.0746

AC:

AN:

134

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0517

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.191

AC:

29138

AN:

152192

Hom.:

5019

Cov.:

AF XY:

0.185

AC XY:

13802

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.464

AC:

19234

AN:

41458

American (AMR)

AF:

0.165

AC:

2517

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

414

AN:

3468

East Asian (EAS)

AF:

0.0562

AC:

292

AN:

5194

South Asian (SAS)

AF:

0.0969

AC:

468

AN:

4830

European-Finnish (FIN)

AF:

0.0254

AC:

270

AN:

10624

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0801

AC:

5444

AN:

68000

Other (OTH)

AF:

0.179

AC:

378

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

982

1964

2947

3929

4911

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.164

Hom.:

751

Bravo

AF:

0.212

Asia WGS

AF:

0.136

AC:

474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.22

(source)

DANN

Benign

0.54

PhyloP100

-0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Computational scores

Splicing

Publications

Other links and lift over