Genetic Variant WAKMAR2:n.225C>G (chr6-137858024-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000448942.5(WAKMAR2):n.225C>G 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 152,206 control chromosomes in the GnomAD database, including 5,009 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 ( 5009 hom., cov: 32)

Exomes 𝑓: 0.080 ( 0 hom. )

Consequence

WAKMAR2
ENST00000448942.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Publications

11 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1 link	n.1056+7135C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WAKMAR2	ENST00000448942.5 link	n.225C>G	non_coding_transcript_exon_variant	Exon 4 of 4	5
WAKMAR2	ENST00000606327.1 link	n.25C>G	non_coding_transcript_exon_variant	Exon 1 of 2	3
WAKMAR2	ENST00000607671.1 link	n.225C>G	non_coding_transcript_exon_variant	Exon 4 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

28979

AN:

151950

Hom.:

4984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0443

Gnomad SAS

AF:

0.0983

Gnomad FIN

AF:

0.0253

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0800

Gnomad OTH

AF:

0.175

GnomAD4 exome

AF:

0.0797

AC:

AN:

138

Hom.:

Cov.:

AF XY:

0.0526

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.0797

AC:

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)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

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:

29056

AN:

152068

Hom.:

5009

Cov.:

AF XY:

0.185

AC XY:

13747

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.465

AC:

19256

AN:

41414

American (AMR)

AF:

0.162

AC:

2476

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

414

AN:

3470

East Asian (EAS)

AF:

0.0446

AC:

231

AN:

5182

South Asian (SAS)

AF:

0.0975

AC:

470

AN:

4820

European-Finnish (FIN)

AF:

0.0253

AC:

268

AN:

10592

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0800

AC:

5436

AN:

67984

Other (OTH)

AF:

0.179

AC:

379

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

979

1959

2938

3918

4897

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.0362

Hom.:

Bravo

AF:

0.212

Asia WGS

AF:

0.133

AC:

465

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.30

(source)

DANN

Benign

0.61

PhyloP100

-1.2

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