GeneBe

NM_001311175.2:c.34G>T

Variant names:

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

Scores

3
3
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.54

Publications

0 publications found
Variant links:
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)

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ACMG classification

Classification was made for transcript

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
TNFAIP8L3NM_001311175.2 linkc.34G>T p.Glu12* stop_gained Exon 1 of 2 ENST00000637513.2 NP_001298104.1 Q5GJ75A0A1B0GTK8
TNFAIP8L3NM_207381.4 linkc.298G>T p.Glu100* stop_gained Exon 2 of 3 NP_997264.2 Q5GJ75
MIR4713HGNR_146310.1 linkn.194+56881C>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNFAIP8L3ENST00000637513.2 linkc.34G>T p.Glu12* stop_gained Exon 1 of 2 1 NM_001311175.2 ENSP00000489743.1 A0A1B0GTK8

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

Publications

Other links and lift over

dbSNP: rs867642638; hg19: chr15-51386759; API