rs11970361

Positions:

• chr6-137857999-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.1056+7160G>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 0.0693 in 152,348 control chromosomes in the GnomAD database, including 472 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 0.069 (472 hom., cov: 32)
  • Exomes 𝑓: 0.051 (0 hom.)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1056+7160G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+7160G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0692 AC: 10530 AN: 152092 Hom.: 465 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.00848

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0674

GnomAD4 exome AF: 0.0507 AC: 7 AN: 138 Hom.: 0 Cov.: 0 AF XY: 0.0395 AC XY: 3 AN XY: 76

Gnomad4 EAS exome AF: 0.0507

GnomAD4 genome AF: 0.0693 AC: 10553 AN: 152210 Hom.: 472 Cov.: 32 AF XY: 0.0671 AC XY: 4992 AN XY: 74422

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.00848

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0583 Hom.: 251

Bravo AF: 0.0763

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11970361; hg19: chr6-138179136;