Genetic Variant ENST00000606998.2: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

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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