rs9494886

chr6-137863193-C-G

Variant summary

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

The NR_049793.1(WAKMAR2):n.1056+1966G>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 0.188 in 152,164 control chromosomes in the GnomAD database, including 4,786 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 (4786 hom., cov: 32)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAKMAR2	NR_049793.1	n.1056+1966G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+1966G>C		intron_variant, non_coding_transcript_variant		2
WAKMAR2	ENST00000448942.5	n.64-268G>C		intron_variant, non_coding_transcript_variant		5
WAKMAR2	ENST00000607671.1	n.64-268G>C		intron_variant, non_coding_transcript_variant		5
WAKMAR2	ENST00000662141.1	n.605-268G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28559 AN: 152046 Hom.: 4767 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.173

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28627 AN: 152164 Hom.: 4786 Cov.: 32 AF XY: 0.182 AC XY: 13557 AN XY: 74382

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0622

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.177

Alfa AF: 0.140 Hom.: 381

Bravo AF: 0.208

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	13
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494886; hg19: chr6-138184330; COSMIC: COSV52797642;