6-137851246-T-C

Variant names:

• chr6-137851246-T-C
• rs600144
• ENST00000606998.2:n.1056+13913A>G

Variant summary

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

The ENST00000606998.2(WAKMAR2):​n.1056+13913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,234 control chromosomes in the GnomAD database, including 2,699 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 0.17 (2699 hom., cov: 32)
• Consequence: WAKMAR2 ENST00000606998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

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+13913A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000606998.2	TSL:2	n.1056+13913A>G		intron	N/A
	WAKMAR2	ENST00000763029.1		n.592+16396A>G		intron	N/A
	WAKMAR2	ENST00000763030.1		n.187+4142A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25820 AN: 152116 Hom.: 2701 Cov.: 32

Gnomad AFR AF: 0.0505

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.170 AC: 25808 AN: 152234 Hom.: 2699 Cov.: 32 AF XY: 0.164 AC XY: 12221 AN XY: 74434

African (AFR) AF: 0.0503 AC: 2092 AN: 41562

American (AMR) AF: 0.178 AC: 2729 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 799 AN: 3466

East Asian (EAS) AF: 0.169 AC: 876 AN: 5180

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1922 AN: 10590

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16476 AN: 67994

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.223 Hom.: 5459

Bravo AF: 0.167

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.78
PhyloP100		-0.58

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: rs600144;

hg19: chr6-138172383;