6-137852285-A-C

Position:

• chr6-137852285-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_049793.1(WAKMAR2):​n.1056+12874T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,032 control chromosomes in the GnomAD database, including 4,123 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 0.18 (4123 hom., cov: 32)
• Consequence: WAKMAR2 NR_049793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

WAKMAR2 (HGNC:53754): (wound and keratinocyte migration associated lncRNA 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WAKMAR2	NR_049793.1	n.1056+12874T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000606998.1	n.1056+12874T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27010 AN: 151914 Hom.: 4098 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.178 AC: 27085 AN: 152032 Hom.: 4123 Cov.: 32 AF XY: 0.172 AC XY: 12808 AN XY: 74300

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0798

Gnomad4 OTH AF: 0.169

Alfa AF: 0.136 Hom.: 517

Bravo AF: 0.197

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.082
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753873; hg19: chr6-138173422; COSMIC: COSV74118445;