rs80126770

Variant names:

• chr6-137846946-C-T
• rs80126770
• ENST00000606998.2:n.1056+18213G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000606998.2(WAKMAR2):​n.1056+18213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0225 in 152,056 control chromosomes in the GnomAD database, including 45 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 0.023 (45 hom., cov: 31)
• Consequence: WAKMAR2 ENST00000606998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• 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=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0225 (3425/152056) while in subpopulation SAS AF = 0.0345 (166/4816). AF 95% confidence interval is 0.0302. There are 45 homozygotes in GnomAd4. There are 1641 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606998.2. 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+18213G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000606998.2	TSL:2	n.1056+18213G>A		intron	N/A
	WAKMAR2	ENST00000763029.1		n.592+20696G>A		intron	N/A
	WAKMAR2	ENST00000763030.1		n.187+8442G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0225 AC: 3417 AN: 151938 Hom.: 43 Cov.: 31

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0225 AC: 3425 AN: 152056 Hom.: 45 Cov.: 31 AF XY: 0.0221 AC XY: 1641 AN XY: 74336

African (AFR) AF: 0.0142 AC: 591 AN: 41474

American (AMR) AF: 0.0186 AC: 284 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5176

South Asian (SAS) AF: 0.0345 AC: 166 AN: 4816

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10584

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0275 AC: 1871 AN: 67944

Other (OTH) AF: 0.0200 AC: 42 AN: 2104

Alfa AF: 0.0249 Hom.: 9

Bravo AF: 0.0219

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.43
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs80126770; hg19: chr6-138168083;