rs1045241

chr5-119393591-C-T

Variant summary

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

The NM_014350.4(TNFAIP8):c.*210C>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 0.273 in 549,590 control chromosomes in the GnomAD database, including 21,243 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 0.30 (6968 hom., cov: 33)
  • Exomes 𝑓: 0.26 (14275 hom.)
• Consequence: TNFAIP8 NM_014350.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

TNFAIP8 (HGNC:17260): (TNF alpha induced protein 8) Enables cysteine-type endopeptidase inhibitor activity involved in apoptotic process. Involved in positive regulation of apoptotic process. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFAIP8	NM_014350.4	c.*210C>T		3_prime_UTR_variant	2/2	ENST00000504771.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP8	ENST00000504771.3	c.*210C>T		3_prime_UTR_variant	2/2	1	NM_014350.4
TNFAIP8	ENST00000415806.2	c.*806C>T		3_prime_UTR_variant	3/3	1
TNFAIP8	ENST00000503646.1	c.*210C>T		3_prime_UTR_variant	3/3	2
TNFAIP8	ENST00000513374.1	c.*210C>T		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45426 AN: 151938 Hom.: 6957 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.263 AC: 104537 AN: 397534 Hom.: 14275 Cov.: 5 AF XY: 0.262 AC XY: 54685 AN XY: 208954

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.267

Gnomad4 ASJ exome AF: 0.251

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.235

Gnomad4 FIN exome AF: 0.302

Gnomad4 NFE exome AF: 0.275

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.299 AC: 45469 AN: 152056 Hom.: 6968 Cov.: 33 AF XY: 0.300 AC XY: 22307 AN XY: 74334

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.298

Alfa AF: 0.305 Hom.: 1526

Bravo AF: 0.297

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1045241; hg19: chr5-118729286; COSMIC: COSV57226452; COSMIC: COSV57226452;