rs59693083

chr6-137865395-A-G

Variant summary

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

The NR_049793.1(WAKMAR2):n.895-75T>C 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 0.191 in 152,420 control chromosomes in the GnomAD database, including 5,019 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 (5019 hom., cov: 32)
  • Exomes 𝑓: 0.066 (0 hom.)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAKMAR2	NR_049793.1	n.895-75T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.895-75T>C		intron_variant, non_coding_transcript_variant		2
WAKMAR2	ENST00000448942.5	n.63+2247T>C		intron_variant, non_coding_transcript_variant		5
WAKMAR2	ENST00000607671.1	n.63+2247T>C		intron_variant, non_coding_transcript_variant		5
WAKMAR2	ENST00000662141.1	n.391-23T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29066 AN: 152072 Hom.: 4998 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.0658 AC: 15 AN: 228 Hom.: 0 AF XY: 0.0429 AC XY: 6 AN XY: 140

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.0746

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0517

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.191 AC: 29138 AN: 152192 Hom.: 5019 Cov.: 32 AF XY: 0.185 AC XY: 13802 AN XY: 74438

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0801

Gnomad4 OTH AF: 0.179

Alfa AF: 0.137 Hom.: 478

Bravo AF: 0.212

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.22
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59693083; hg19: chr6-138186532;