6-137850329-A-G

Variant names:

• chr6-137850329-A-G
• rs9494883
• ENST00000606998.2:n.1056+14830T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 13 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 = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606998.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	NR_049793.1		n.1056+14830T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000606998.2	TSL:2	n.1056+14830T>C		intron	N/A
	WAKMAR2	ENST00000763029.1		n.592+17313T>C		intron	N/A
	WAKMAR2	ENST00000763030.1		n.187+5059T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11433 AN: 152096 Hom.: 837 Cov.: 32

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.: 32 AF XY: 0.0736 AC XY: 5481 AN XY: 74440

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: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1975 AN: 68018

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		0.16
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: rs9494883; hg19: chr6-138171466;