rs17145129

Variant names:

• chr5-119304476-A-G
• rs17145129
• ENST00000274456.6:c.1+35569A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000274456.6(TNFAIP8):​c.1+35569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,144 control chromosomes in the GnomAD database, including 3,854 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 0.14 (3854 hom., cov: 32)
• Consequence: TNFAIP8 ENST00000274456.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000274456.6. 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_001077654.3		c.1+35569A>G		intron	N/A	NP_001071122.1
	TNFAIP8	NM_001286815.2		c.-183-11709A>G		intron	N/A	NP_001273744.1
	TNFAIP8	NM_001286817.2		c.-187-11705A>G		intron	N/A	NP_001273746.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8	ENST00000274456.6	TSL:1	c.1+35569A>G		intron	N/A	ENSP00000274456.6
	TNFAIP8	ENST00000388882.5	TSL:4	c.-183-11709A>G		intron	N/A	ENSP00000429432.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20898 AN: 152026 Hom.: 3833 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.00321

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.104

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 20974 AN: 152144 Hom.: 3854 Cov.: 32 AF XY: 0.134 AC XY: 9942 AN XY: 74406

African (AFR) AF: 0.424 AC: 17572 AN: 41442

American (AMR) AF: 0.0644 AC: 984 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3470

East Asian (EAS) AF: 0.0428 AC: 222 AN: 5184

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4824

European-Finnish (FIN) AF: 0.00321 AC: 34 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1478 AN: 68008

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.0676 Hom.: 322

Bravo AF: 0.154

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		1.5

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: rs17145129; hg19: chr5-118640171; COSMIC: COSV57229402; COSMIC: COSV57229402;