5-119340116-C-T

Variant names:

• chr5-119340116-C-T
• rs7719094
• ENST00000274456.6:c.2-52700C>T

Variant summary

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

The ENST00000274456.6(TNFAIP8):​c.2-52700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 152,230 control chromosomes in the GnomAD database, including 415 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 0.068 (415 hom., cov: 32)
• Consequence: TNFAIP8 ENST00000274456.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 3 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]

LOC102723444 (HGNC:):

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 = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723444	XR_001742858.2	n.6675G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723444	XR_007058912.1	n.6759G>A		non_coding_transcript_exon_variant	Exon 5 of 5
TNFAIP8	NM_001286814.1	c.67+6485C>T		intron_variant	Intron 1 of 1		NP_001273743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8	ENST00000274456.6	c.2-52700C>T		intron_variant	Intron 1 of 1	1		ENSP00000274456.6
TNFAIP8	ENST00000513374.1	c.67+6485C>T		intron_variant	Intron 1 of 1	2		ENSP00000427424.1
TNFAIP8	ENST00000388882.5	c.-66+23814C>T		intron_variant	Intron 2 of 2	4		ENSP00000429432.1

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10281 AN: 152112 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0678 AC: 10325 AN: 152230 Hom.: 415 Cov.: 32 AF XY: 0.0693 AC XY: 5158 AN XY: 74422

African (AFR) AF: 0.114 AC: 4720 AN: 41532

American (AMR) AF: 0.0582 AC: 890 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5178

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4828

European-Finnish (FIN) AF: 0.0635 AC: 673 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3025 AN: 68018

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0543 Hom.: 539

Bravo AF: 0.0714

Asia WGS AF: 0.0630 AC: 219 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	1.6
DANN	Benign	0.58
PhyloP100		-0.62
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: rs7719094; hg19: chr5-118675811;