6-137858024-G-C

Variant names:

• chr6-137858024-G-C
• rs11970411
• ENST00000448942.5:n.225C>G

Variant summary

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

The ENST00000606327.1(WAKMAR2):​n.25C>G 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 152,206 control chromosomes in the GnomAD database, including 5,009 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 (5009 hom., cov: 32)
  • Exomes 𝑓: 0.080 (0 hom.)
• Consequence: WAKMAR2 ENST00000606327.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 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+7135C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000448942.5	TSL:5	n.225C>G		non_coding_transcript_exon	Exon 4 of 4
	WAKMAR2	ENST00000606327.1	TSL:3	n.25C>G		non_coding_transcript_exon	Exon 1 of 2
	WAKMAR2	ENST00000607671.1	TSL:5	n.225C>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28979 AN: 151950 Hom.: 4984 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.0797 AC: 11 AN: 138 Hom.: 0 Cov.: 0 AF XY: 0.0526 AC XY: 4 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: 0.0797 AC: 11 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: 0.191 AC: 29056 AN: 152068 Hom.: 5009 Cov.: 32 AF XY: 0.185 AC XY: 13747 AN XY: 74346

African (AFR) AF: 0.465 AC: 19256 AN: 41414

American (AMR) AF: 0.162 AC: 2476 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3470

East Asian (EAS) AF: 0.0446 AC: 231 AN: 5182

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4820

European-Finnish (FIN) AF: 0.0253 AC: 268 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0800 AC: 5436 AN: 67984

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.0362 Hom.: 38

Bravo AF: 0.212

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.61
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11970411; hg19: chr6-138179161;