rs9494883

Positions:

• chr6-137850329-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.1056+14830T>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 0.0753 in 152,214 control chromosomes in the GnomAD database, including 838 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 0.075 (838 hom., cov: 32)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAKMAR2	NR_049793.1	n.1056+14830T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+14830T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11433 AN: 152096 Hom.: 837 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0753 AC: 11460 AN: 152214 Hom.: 838 Cov.: 32 AF XY: 0.0736 AC XY: 5481 AN XY: 74440

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0311

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0398 Hom.: 202

Bravo AF: 0.0823

Asia WGS AF: 0.0400 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494883; hg19: chr6-138171466;