rs1052912

Positions:

• chr14-103137316-G-A

Variant summary

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

The NM_006291.4(TNFAIP2):​c.*1956G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,256 control chromosomes in the GnomAD database, including 1,399 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 0.13 (1398 hom., cov: 33)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: TNFAIP2 NM_006291.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

TNFAIP2 (HGNC:11895): (TNF alpha induced protein 2) This gene was identified as a gene whose expression can be induced by the tumor necrosis factor alpha (TNF) in umbilical vein endothelial cells. The expression of this gene was shown to be induced by retinoic acid in a cell line expressing a oncogenic version of the retinoic acid receptor alpha fusion protein, which suggested that this gene may be a retinoic acid target gene in acute promyelocytic leukemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFAIP2	NM_006291.4	c.*1956G>A		3_prime_UTR_variant	12/12	ENST00000560869.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP2	ENST00000560869.6	c.*1956G>A		3_prime_UTR_variant	12/12	5	NM_006291.4	P1
TNFAIP2	ENST00000333007.8	c.*1956G>A		3_prime_UTR_variant	13/13	1		P1
TNFAIP2	ENST00000561217.1	n.487G>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19405 AN: 152098 Hom.: 1398 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.125 AC: 5 AN: 40 Hom.: 1 Cov.: 0 AF XY: 0.0714 AC XY: 2 AN XY: 28

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.128 AC: 19427 AN: 152216 Hom.: 1398 Cov.: 33 AF XY: 0.125 AC XY: 9330 AN XY: 74418

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.111

Alfa AF: 0.114 Hom.: 1407

Bravo AF: 0.132

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.7
DANN	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1052912; hg19: chr14-103603653;