6-137856321-T-G

Variant names:

• chr6-137856321-T-G
• rs7767264
• ENST00000606327.1:n.323-836A>C

Variant summary

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

The ENST00000606327.1(WAKMAR2):​n.323-836A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,942 control chromosomes in the GnomAD database, including 5,117 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 (5117 hom., cov: 31)
• Consequence: WAKMAR2 ENST00000606327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1056+8838A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606327.1	n.323-836A>C		intron_variant	Intron 1 of 1	3
WAKMAR2	ENST00000606998.2	n.1056+8838A>C		intron_variant	Intron 3 of 3	2
WAKMAR2	ENST00000662141.1	n.985-836A>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29268 AN: 151824 Hom.: 5090 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.193 AC: 29348 AN: 151942 Hom.: 5117 Cov.: 31 AF XY: 0.187 AC XY: 13897 AN XY: 74292

African (AFR) AF: 0.470 AC: 19455 AN: 41358

American (AMR) AF: 0.163 AC: 2484 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3472

East Asian (EAS) AF: 0.0631 AC: 327 AN: 5180

South Asian (SAS) AF: 0.102 AC: 490 AN: 4808

European-Finnish (FIN) AF: 0.0235 AC: 249 AN: 10598

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

European-Non Finnish (NFE) AF: 0.0798 AC: 5422 AN: 67934

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.0249 Hom.: 18

Bravo AF: 0.214

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.67
PhyloP100		-0.42
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: rs7767264; hg19: chr6-138177458; COSMIC: COSV70566466;