rs7719094

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-119340116-C-G
• chr5-119340116-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000274456.6(TNFAIP8):​c.2-52700C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723444	XR_001742858.2	n.6675G>C		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723444	XR_007058912.1	n.6759G>C		non_coding_transcript_exon_variant	Exon 5 of 5
TNFAIP8	NM_001286814.1	c.67+6485C>G		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>G		intron_variant	Intron 1 of 1	1		ENSP00000274456.6
TNFAIP8	ENST00000513374.1	c.67+6485C>G		intron_variant	Intron 1 of 1	2		ENSP00000427424.1
TNFAIP8	ENST00000388882.5	c.-66+23814C>G		intron_variant	Intron 2 of 2	4		ENSP00000429432.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.62

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;