rs867642638

Variant names:

• chr15-51094562-C-A
• rs867642638
• NM_001311175.2:c.34G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-51094562-C-A
• chr15-51094562-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001311175.2(TNFAIP8L3):​c.34G>T​(p.Glu12*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNFAIP8L3 NM_001311175.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.54
• Publications: 0 publications found

Genes affected

TNFAIP8L3 (HGNC:20620): (TNF alpha induced protein 8 like 3) Predicted to enable phosphatidylinositol binding activity and phosphatidylinositol transfer activity. Predicted to be involved in several processes, including inositol lipid-mediated signaling; positive regulation of intracellular signal transduction; and positive regulation of phosphatidylinositol 3-kinase activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MIR4713HG (HGNC:53124): (MIR4713 host gene)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP8L3	NM_001311175.2	c.34G>T	p.Glu12*	stop_gained	Exon 1 of 2	ENST00000637513.2	NP_001298104.1
TNFAIP8L3	NM_207381.4	c.298G>T	p.Glu100*	stop_gained	Exon 2 of 3		NP_997264.2
MIR4713HG	NR_146310.1	n.194+56881C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8L3	ENST00000637513.2	c.34G>T	p.Glu12*	stop_gained	Exon 1 of 2	1	NM_001311175.2	ENSP00000489743.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1350204 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 667044

African (AFR) AF: 0.00 AC: 0 AN: 27680

American (AMR) AF: 0.00 AC: 0 AN: 33618

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23888

East Asian (EAS) AF: 0.00 AC: 0 AN: 29656

South Asian (SAS) AF: 0.00 AC: 0 AN: 76778

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34742

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5348

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1062470

Other (OTH) AF: 0.00 AC: 0 AN: 56024

GnomAD4 genome Cov.: 33

Alfa AF: 0.000219 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.53
CADD	Pathogenic	41
DANN	Uncertain	0.99
Eigen	Pathogenic	0.71
Eigen_PC	Uncertain	0.48
FATHMM_MKL	Uncertain	0.82	D
PhyloP100		2.5
Vest4		0.078
GERP RS		3.8
PromoterAI		-0.0011	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs867642638; hg19: chr15-51386759;