rs670369

Positions:

• chr6-137825911-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_049793.1(WAKMAR2):​n.1057-1334G>A variant causes a intron, non coding transcript 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 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1057-1334G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1057-1334G>A		intron_variant, non_coding_transcript_variant		2
WAKMAR2	ENST00000440578.1			upstream_gene_variant		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

Gnomad4 EAS exome AF: 0.826

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.739

Alfa AF: 0.815 Hom.: 67068

Bravo AF: 0.690

Asia WGS AF: 0.842 AC: 2925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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