Genetic Variant WAKMAR2:n.575G>A (chr6-137825911-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000440578.2(WAKMAR2):n.575G>A 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 0.708 in 152,162 control chromosomes in the GnomAD database, including 41,349 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 0.71 ( 41301 hom., cov: 30)

Exomes 𝑓: 0.83 ( 48 hom. )

Consequence

WAKMAR2
ENST00000440578.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

Publications

9 publications found

Variant links:

COSMIC-nc: COSV71213160

Genes affected

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

WAKMAR2 links:

ENSG00000299400 (HGNC:):

ENSG00000299400 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1 link	n.1057-1334G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WAKMAR2	ENST00000440578.2 link	n.575G>A	non_coding_transcript_exon_variant	Exon 3 of 4	3
WAKMAR2	ENST00000763037.1 link	n.85G>A	non_coding_transcript_exon_variant	Exon 2 of 3
WAKMAR2	ENST00000763039.1 link	n.304G>A	non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107519

AN:

151904

Hom.:

41298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.924

Gnomad AMR

AF:

0.807

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.894

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.823

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.839

Gnomad OTH

AF:

0.738

GnomAD4 exome

AF:

0.829

AC:

116

AN:

140

Hom.:

Cov.:

AF XY:

0.910

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.826

AC:

114

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.707

AC:

107550

AN:

152022

Hom.:

41301

Cov.:

AF XY:

0.711

AC XY:

52830

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.373

AC:

15443

AN:

41390

American (AMR)

AF:

0.807

AC:

12332

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.785

AC:

2722

AN:

3468

East Asian (EAS)

AF:

0.894

AC:

4633

AN:

5182

South Asian (SAS)

AF:

0.843

AC:

4061

AN:

4820

European-Finnish (FIN)

AF:

0.823

AC:

8709

AN:

10584

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.839

AC:

57040

AN:

67996

Other (OTH)

AF:

0.739

AC:

1557

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1266

2532

3797

5063

6329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.802

Hom.:

82586

Bravo

AF:

0.690

Asia WGS

AF:

0.842

AC:

2925

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.35

(source)

DANN

Benign

0.52

PhyloP100

-1.8

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