NM_001311175.2:c.-109_-101dupCGCCGCCCG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001311175.2(TNFAIP8L3):​c.-109_-101dupCGCCGCCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000532 in 1,062,408 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00061 ( 2 hom., cov: 27)
Exomes 𝑓: 0.00052 ( 2 hom. )

Consequence

TNFAIP8L3
NM_001311175.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640
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 made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TNFAIP8L3NM_001311175.2 linkc.-109_-101dupCGCCGCCCG 5_prime_UTR_variant Exon 1 of 2 ENST00000637513.2 NP_001298104.1 Q5GJ75A0A1B0GTK8
TNFAIP8L3NM_207381.4 linkc.173-17_173-9dupCGCCGCCCG intron_variant Intron 1 of 2 NP_997264.2 Q5GJ75
MIR4713HGNR_146310.1 linkn.194+57029_194+57037dupGGCGCGGGC intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNFAIP8L3ENST00000637513.2 linkc.-109_-101dupCGCCGCCCG 5_prime_UTR_variant Exon 1 of 2 1 NM_001311175.2 ENSP00000489743.1 A0A1B0GTK8
TNFAIP8L3ENST00000327536.5 linkc.173-17_173-9dupCGCCGCCCG intron_variant Intron 1 of 2 1 ENSP00000328016.5 Q5GJ75
MIR4713HGENST00000559909.1 linkn.194+57029_194+57037dupGGCGCGGGC intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.000606
AC:
89
AN:
146826
Hom.:
2
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.000342
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00115
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000393
Gnomad SAS
AF:
0.00291
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00962
Gnomad NFE
AF:
0.000560
Gnomad OTH
AF:
0.000987
GnomAD4 exome
AF:
0.000519
AC:
475
AN:
915474
Hom.:
2
Cov.:
4
AF XY:
0.000554
AC XY:
238
AN XY:
429590
show subpopulations
Gnomad4 AFR exome
AF:
0.000112
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000130
Gnomad4 EAS exome
AF:
0.000105
Gnomad4 SAS exome
AF:
0.00369
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000450
Gnomad4 OTH exome
AF:
0.000653
GnomAD4 genome
AF:
0.000613
AC:
90
AN:
146934
Hom.:
2
Cov.:
27
AF XY:
0.000503
AC XY:
36
AN XY:
71506
show subpopulations
Gnomad4 AFR
AF:
0.000341
Gnomad4 AMR
AF:
0.00115
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000394
Gnomad4 SAS
AF:
0.00312
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000560
Gnomad4 OTH
AF:
0.000977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201887319; hg19: chr15-51386892; API