6-137851611-T-C

Variant names:

• chr6-137851611-T-C
• rs9494885
• ENST00000606998.2:n.1056+13548A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606998.2(WAKMAR2):​n.1056+13548A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,154 control chromosomes in the GnomAD database, including 5,140 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 (5140 hom., cov: 32)
• Consequence: WAKMAR2 ENST00000606998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 28 publications found

Genes affected

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

ENSG00000299400 (HGNC:):

ACMG classification

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 = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1056+13548A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.2	n.1056+13548A>G		intron_variant	Intron 3 of 3	2
WAKMAR2	ENST00000763029.1	n.592+16031A>G		intron_variant	Intron 1 of 1
WAKMAR2	ENST00000763030.1	n.187+3777A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29308 AN: 152036 Hom.: 5112 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.193 AC: 29391 AN: 152154 Hom.: 5140 Cov.: 32 AF XY: 0.187 AC XY: 13912 AN XY: 74418

African (AFR) AF: 0.471 AC: 19513 AN: 41448

American (AMR) AF: 0.163 AC: 2487 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3470

East Asian (EAS) AF: 0.0561 AC: 291 AN: 5188

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4822

European-Finnish (FIN) AF: 0.0253 AC: 269 AN: 10624

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0799 AC: 5436 AN: 67994

Other (OTH) AF: 0.184 AC: 388 AN: 2114

Alfa AF: 0.131 Hom.: 1028

Bravo AF: 0.214

Asia WGS AF: 0.139 AC: 485 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	1.6
DANN	Benign	0.52
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9494885; hg19: chr6-138172748; COSMIC: COSV74118443;