chr5-119369850-T-G

Variant names:

• chr5-119369850-T-G
• rs32652
• NM_014350.4:c.31+13729T>G

Variant summary

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

The NM_014350.4(TNFAIP8):​c.31+13729T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,116 control chromosomes in the GnomAD database, including 44,625 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 0.76 (44625 hom., cov: 32)
• Consequence: TNFAIP8 NM_014350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP8	NM_014350.4	c.31+13729T>G		intron_variant	Intron 1 of 1	ENST00000504771.3	NP_055165.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8	ENST00000504771.3	c.31+13729T>G		intron_variant	Intron 1 of 1	1	NM_014350.4	ENSP00000422245.1

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115215 AN: 151998 Hom.: 44572 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.758 AC: 115323 AN: 152116 Hom.: 44625 Cov.: 32 AF XY: 0.756 AC XY: 56219 AN XY: 74358

African (AFR) AF: 0.934 AC: 38778 AN: 41522

American (AMR) AF: 0.684 AC: 10449 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3132 AN: 5156

South Asian (SAS) AF: 0.764 AC: 3684 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7310 AN: 10566

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.700 AC: 47563 AN: 67982

Other (OTH) AF: 0.719 AC: 1517 AN: 2110

Alfa AF: 0.717 Hom.: 19884

Bravo AF: 0.761

Asia WGS AF: 0.679 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		0.027
Mutation Taster		=100/0	polymorphism (auto)

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: rs32652; hg19: chr5-118705545;