rs11970361

Variant names:

• chr6-137857999-C-T
• rs11970361
• ENST00000448942.5:n.250G>A

Variant summary

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

The ENST00000606327.1(WAKMAR2):​n.50G>A 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 0.0693 in 152,348 control chromosomes in the GnomAD database, including 472 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 0.069 (472 hom., cov: 32)
  • Exomes 𝑓: 0.051 (0 hom.)
• Consequence: WAKMAR2 ENST00000606327.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 6 publications found

Genes affected

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

ENSG00000299400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606327.1. 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.1056+7160G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000448942.5	TSL:5	n.250G>A		non_coding_transcript_exon	Exon 4 of 4
	WAKMAR2	ENST00000606327.1	TSL:3	n.50G>A		non_coding_transcript_exon	Exon 1 of 2
	WAKMAR2	ENST00000607671.1	TSL:5	n.250G>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0692 AC: 10530 AN: 152092 Hom.: 465 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.00848

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0674

GnomAD4 exome AF: 0.0507 AC: 7 AN: 138 Hom.: 0 Cov.: 0 AF XY: 0.0395 AC XY: 3 AN XY: 76

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0507 AC: 7 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0693 AC: 10553 AN: 152210 Hom.: 472 Cov.: 32 AF XY: 0.0671 AC XY: 4992 AN XY: 74422

African (AFR) AF: 0.116 AC: 4817 AN: 41528

American (AMR) AF: 0.0921 AC: 1407 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5184

South Asian (SAS) AF: 0.0659 AC: 317 AN: 4812

European-Finnish (FIN) AF: 0.00848 AC: 90 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0490 AC: 3331 AN: 68004

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0612 Hom.: 358

Bravo AF: 0.0763

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		-0.23
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: rs11970361;

hg19: chr6-138179136;