rs10519585

Positions:

• chr5-119340834-T-C

Variant summary

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

The ENST00000274456.6(TNFAIP8):​c.2-51982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,992 control chromosomes in the GnomAD database, including 10,494 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 0.36 (10494 hom., cov: 31)
• Consequence: TNFAIP8 ENST00000274456.6 intron
• 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]

LOC102723444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723444	XR_001742858.2	n.5957A>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP8	ENST00000274456.6	c.2-51982T>C		intron_variant		1		P1
TNFAIP8	ENST00000388882.5	c.-66+24532T>C		intron_variant		4
TNFAIP8	ENST00000513374.1	c.67+7203T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54103 AN: 151874 Hom.: 10479 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.356 AC: 54174 AN: 151992 Hom.: 10494 Cov.: 31 AF XY: 0.356 AC XY: 26424 AN XY: 74286

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.321

Alfa AF: 0.314 Hom.: 10813

Bravo AF: 0.358

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519585; hg19: chr5-118676529; COSMIC: COSV57226161;