rs670369

Variant names:

• chr6-137825911-C-T
• rs670369
• ENST00000440578.2:n.575G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440578.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	NR_049793.1		n.1057-1334G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000440578.2	TSL:3	n.575G>A		non_coding_transcript_exon	Exon 3 of 4
	WAKMAR2	ENST00000763037.1		n.85G>A		non_coding_transcript_exon	Exon 2 of 3
	WAKMAR2	ENST00000763039.1		n.304G>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107519 AN: 151904 Hom.: 41298 Cov.: 30

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.: 48 Cov.: 0 AF XY: 0.910 AC XY: 71 AN XY: 78

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.826 AC: 114 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.707 AC: 107550 AN: 152022 Hom.: 41301 Cov.: 30 AF XY: 0.711 AC XY: 52830 AN XY: 74314

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs670369; hg19: chr6-138147048; COSMIC: COSV71213160;