6-137851246-T-C

Position:

• chr6-137851246-T-C

Variant summary

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

The NR_049793.1(WAKMAR2):​n.1056+13913A>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 0.17 in 152,234 control chromosomes in the GnomAD database, including 2,699 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 0.17 (2699 hom., cov: 32)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAKMAR2	NR_049793.1	n.1056+13913A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+13913A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25820 AN: 152116 Hom.: 2701 Cov.: 32

Gnomad AFR AF: 0.0505

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.170 AC: 25808 AN: 152234 Hom.: 2699 Cov.: 32 AF XY: 0.164 AC XY: 12221 AN XY: 74434

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.201

Alfa AF: 0.222 Hom.: 4023

Bravo AF: 0.167

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs600144; hg19: chr6-138172383;