5-119395172-G-A

Position:

• chr5-119395172-G-A

Variant summary

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

The NM_014350.4(TNFAIP8):​c.*1791G>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 0.656 in 152,066 control chromosomes in the GnomAD database, including 33,638 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 0.66 (33634 hom., cov: 31)
  • Exomes 𝑓: 0.80 (4 hom.)
• Consequence: TNFAIP8 NM_014350.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFAIP8	NM_014350.4	c.*1791G>A		3_prime_UTR_variant	2/2	ENST00000504771.3	NP_055165.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFAIP8	ENST00000504771.3	c.*1791G>A		3_prime_UTR_variant	2/2	1	NM_014350.4	ENSP00000422245

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99693 AN: 151938 Hom.: 33615 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.649

GnomAD4 exome AF: 0.800 AC: 8 AN: 10 Hom.: 4 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

Gnomad4 NFE exome AF: 0.800

GnomAD4 genome AF: 0.656 AC: 99761 AN: 152056 Hom.: 33634 Cov.: 31 AF XY: 0.647 AC XY: 48110 AN XY: 74336

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.650

Alfa AF: 0.676 Hom.: 21604

Bravo AF: 0.649

Asia WGS AF: 0.443 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6893184; hg19: chr5-118730867;