rs1052912

Variant names:

• chr14-103137316-G-A
• rs1052912
• NM_006291.4:c.*1956G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006291.4. 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
	TNFAIP2	NM_006291.4	MANE Select	c.*1956G>A		3_prime_UTR	Exon 12 of 12	NP_006282.2
	TNFAIP2	NM_001371220.1		c.*1313G>A		3_prime_UTR	Exon 13 of 13	NP_001358149.1
	TNFAIP2	NM_001371221.1		c.*1313G>A		3_prime_UTR	Exon 13 of 13	NP_001358150.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP2	ENST00000560869.6	TSL:5 MANE Select	c.*1956G>A		3_prime_UTR	Exon 12 of 12	ENSP00000452634.2
	TNFAIP2	ENST00000333007.8	TSL:1	c.*1956G>A		3_prime_UTR	Exon 13 of 13	ENSP00000332326.1
	TNFAIP2	ENST00000903839.1		c.*1956G>A		3_prime_UTR	Exon 14 of 14	ENSP00000573898.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 5 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.194 AC: 8043 AN: 41502

American (AMR) AF: 0.108 AC: 1649 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0799 AC: 386 AN: 4830

European-Finnish (FIN) AF: 0.0930 AC: 986 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7582 AN: 68016

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.116 Hom.: 1868

Bravo AF: 0.132

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1052912; hg19: chr14-103603653;