rs9494885

Positions:

• chr6-137851611-T-C
• chr6-137851611-T-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+13548A>G 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 0.193 in 152,154 control chromosomes in the GnomAD database, including 5,140 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 (5140 hom., cov: 32)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

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 = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1056+13548A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+13548A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29308 AN: 152036 Hom.: 5112 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.193 AC: 29391 AN: 152154 Hom.: 5140 Cov.: 32 AF XY: 0.187 AC XY: 13912 AN XY: 74418

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0561

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.184

Alfa AF: 0.119 Hom.: 529

Bravo AF: 0.214

Asia WGS AF: 0.139 AC: 485 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	1.6
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: rs9494885; hg19: chr6-138172748; COSMIC: COSV74118443;