rs5029924

Variant names:

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

Variant summary

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

The XM_011536095.2(TNFAIP3):​c.-321C>T variant causes a 5 prime UTR 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: TNFAIP3 XM_011536095.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP3	XM_011536095.2	c.-321C>T		5_prime_UTR_variant	Exon 1 of 10		XP_011534397.1
TNFAIP3	XM_047419283.1	c.-627C>T		5_prime_UTR_variant	Exon 1 of 9		XP_047275239.1
WAKMAR2	NR_049793.1	n.894+222G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WAKMAR2	ENST00000448942.5	n.63+1281G>A		intron_variant	Intron 1 of 3	5
WAKMAR2	ENST00000606998.1	n.894+222G>A		intron_variant	Intron 2 of 3	2
WAKMAR2	ENST00000607671.1	n.63+1281G>A		intron_variant	Intron 1 of 3	5
WAKMAR2	ENST00000662141.1	n.390+222G>A		intron_variant	Intron 2 of 6

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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0312

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0844 Hom.: 182

Bravo AF: 0.135

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5029924; hg19: chr6-138187498;