ENST00000606998.2:n.4034T>C

Variant names:

• chr6-137821600-A-G
• rs2788289
• ENST00000606998.2:n.4034T>C

Variant summary

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

The ENST00000606998.2(WAKMAR2):​n.4034T>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 0.686 in 152,138 control chromosomes in the GnomAD database, including 39,704 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 0.69 (39704 hom., cov: 32)
• Consequence: WAKMAR2 ENST00000606998.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.2	n.4034T>C		non_coding_transcript_exon_variant	Exon 4 of 4	2
ENSG00000299400	ENST00000763184.1	n.338+1163A>G		intron_variant	Intron 2 of 2
ENSG00000299400	ENST00000763185.1	n.331+1163A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104405 AN: 152020 Hom.: 39712 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.686 AC: 104407 AN: 152138 Hom.: 39704 Cov.: 32 AF XY: 0.689 AC XY: 51243 AN XY: 74378

African (AFR) AF: 0.324 AC: 13432 AN: 41498

American (AMR) AF: 0.756 AC: 11556 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2724 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4558 AN: 5180

South Asian (SAS) AF: 0.812 AC: 3914 AN: 4822

European-Finnish (FIN) AF: 0.821 AC: 8681 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56993 AN: 67996

Other (OTH) AF: 0.712 AC: 1498 AN: 2104

Alfa AF: 0.733 Hom.: 8514

Bravo AF: 0.666

Asia WGS AF: 0.759 AC: 2639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.64
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2788289; hg19: chr6-138142737;