rs5029924

Variant names:

• chr6-137866361-C-T
• rs5029924
• XM_011536095.2:c.-321C>T

Variant summary

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

The ENST00000763056.1(WAKMAR2):​n.610G>A 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 0.121 in 152,172 control chromosomes in the GnomAD database, including 2,586 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 0.12 (2586 hom., cov: 32)
• Consequence: WAKMAR2 ENST00000763056.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 24 publications found

Genes affected

TNFAIP3 (HGNC:11896): (TNF alpha induced protein 3) This gene was identified as a gene whose expression is rapidly induced by the tumor necrosis factor (TNF). The protein encoded by this gene is a zinc finger protein and ubiqitin-editing enzyme, and has been shown to inhibit NF-kappa B activation as well as TNF-mediated apoptosis. The encoded protein, which has both ubiquitin ligase and deubiquitinase activities, is involved in the cytokine-mediated immune and inflammatory responses. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2012]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763056.1. 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.894+222G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAKMAR2	ENST00000763056.1		n.610G>A		non_coding_transcript_exon	Exon 2 of 2
	WAKMAR2	ENST00000763058.1		n.675G>A		non_coding_transcript_exon	Exon 1 of 1
	WAKMAR2	ENST00000448942.5	TSL:5	n.63+1281G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18403 AN: 152054 Hom.: 2570 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.121 AC: 18465 AN: 152172 Hom.: 2586 Cov.: 32 AF XY: 0.117 AC XY: 8721 AN XY: 74388

African (AFR) AF: 0.345 AC: 14320 AN: 41458

American (AMR) AF: 0.0731 AC: 1118 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5180

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4822

European-Finnish (FIN) AF: 0.0166 AC: 176 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0312 AC: 2122 AN: 68010

Other (OTH) AF: 0.115 AC: 243 AN: 2110

Alfa AF: 0.0945 Hom.: 235

Bravo AF: 0.135

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.78
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

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: rs5029924;

hg19: chr6-138187498;