rs59693083

Variant names:

• chr6-137865395-A-G
• rs59693083
• ENST00000763036.1:n.160T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000763036.1(WAKMAR2):​n.160T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,420 control chromosomes in the GnomAD database, including 5,019 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 (5019 hom., cov: 32)
  • Exomes 𝑓: 0.066 (0 hom.)
• Consequence: WAKMAR2 ENST00000763036.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 9 publications found

Genes affected

WAKMAR2 (HGNC:53754): (wound and keratinocyte migration associated lncRNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763036.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	NR_049793.1		n.895-75T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000763036.1		n.160T>C		non_coding_transcript_exon	Exon 1 of 3
	WAKMAR2	ENST00000763056.1		n.1576T>C		non_coding_transcript_exon	Exon 2 of 2
	WAKMAR2	ENST00000763058.1		n.1641T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29066 AN: 152072 Hom.: 4998 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.0658 AC: 15 AN: 228 Hom.: 0 AF XY: 0.0429 AC XY: 6 AN XY: 140

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0746 AC: 10 AN: 134

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0517 AC: 3 AN: 58

Other (OTH) AF: 0.167 AC: 2 AN: 12

GnomAD4 genome AF: 0.191 AC: 29138 AN: 152192 Hom.: 5019 Cov.: 32 AF XY: 0.185 AC XY: 13802 AN XY: 74438

African (AFR) AF: 0.464 AC: 19234 AN: 41458

American (AMR) AF: 0.165 AC: 2517 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.0562 AC: 292 AN: 5194

South Asian (SAS) AF: 0.0969 AC: 468 AN: 4830

European-Finnish (FIN) AF: 0.0254 AC: 270 AN: 10624

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0801 AC: 5444 AN: 68000

Other (OTH) AF: 0.179 AC: 378 AN: 2112

Alfa AF: 0.164 Hom.: 751

Bravo AF: 0.212

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.54
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs59693083;

hg19: chr6-138186532;