14-103137232-C-T

Position:

• chr14-103137232-C-T

Variant summary

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

The NM_006291.4(TNFAIP2):​c.*1872C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,108 control chromosomes in the GnomAD database, including 30,712 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 0.63 (30712 hom., cov: 33)
  • Exomes 𝑓: 0.66 (36 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNFAIP2 NM_006291.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFAIP2	NM_006291.4	c.*1872C>T		3_prime_UTR_variant	12/12	ENST00000560869.6	NP_006282.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFAIP2	ENST00000560869.6	c.*1872C>T		3_prime_UTR_variant	12/12	5	NM_006291.4	ENSP00000452634.2
TNFAIP2	ENST00000333007.8	c.*1872C>T		3_prime_UTR_variant	13/13	1		ENSP00000332326.1
TNFAIP2	ENST00000561217.1	n.403C>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96136 AN: 151992 Hom.: 30684 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.660

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.656 AC: 105 AN: 160 Hom.: 36 Cov.: 0 AF XY: 0.667 AC XY: 56 AN XY: 84

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.682

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.571

Gnomad4 NFE exome AF: 0.660

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.633 AC: 96211 AN: 152108 Hom.: 30712 Cov.: 33 AF XY: 0.623 AC XY: 46324 AN XY: 74348

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.664

Alfa AF: 0.722 Hom.: 18585

Bravo AF: 0.637

Asia WGS AF: 0.713 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.73

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: rs8126; hg19: chr14-103603569;