chr5-119395172-G-A

Variant names:

• chr5-119395172-G-A
• rs6893184
• NM_014350.4:c.*1791G>A

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014350.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8	NM_014350.4	MANE Select	c.*1791G>A		3_prime_UTR	Exon 2 of 2	NP_055165.2
	TNFAIP8	NM_001286813.2		c.*1791G>A		3_prime_UTR	Exon 3 of 3	NP_001273742.1
	TNFAIP8	NM_001077654.3		c.*1791G>A		3_prime_UTR	Exon 2 of 2	NP_001071122.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8	ENST00000504771.3	TSL:1 MANE Select	c.*1791G>A		3_prime_UTR	Exon 2 of 2	ENSP00000422245.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 8 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.710 AC: 29442 AN: 41466

American (AMR) AF: 0.575 AC: 8780 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3466

East Asian (EAS) AF: 0.150 AC: 774 AN: 5176

South Asian (SAS) AF: 0.631 AC: 3038 AN: 4814

European-Finnish (FIN) AF: 0.613 AC: 6484 AN: 10576

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47022 AN: 67962

Other (OTH) AF: 0.650 AC: 1371 AN: 2110

Alfa AF: 0.667 Hom.: 37066

Bravo AF: 0.649

Asia WGS AF: 0.443 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6893184; hg19: chr5-118730867;