rs5743947

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000317204.11(TOLLIP):​c.184-2025G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0234 in 152,294 control chromosomes in the GnomAD database, including 337 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 0.023 ( 337 hom., cov: 33)

Consequence

TOLLIP
ENST00000317204.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.958
Variant links:
Genes affected
TOLLIP (HGNC:16476): (toll interacting protein) This gene encodes a ubiquitin-binding protein that interacts with several Toll-like receptor (TLR) signaling cascade components. The encoded protein regulates inflammatory signaling and is involved in interleukin-1 receptor trafficking and in the turnover of IL1R-associated kinase. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TOLLIPNM_019009.4 linkuse as main transcriptc.184-2025G>A intron_variant ENST00000317204.11 NP_061882.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TOLLIPENST00000317204.11 linkuse as main transcriptc.184-2025G>A intron_variant 1 NM_019009.4 ENSP00000314733 P1Q9H0E2-1

Frequencies

GnomAD3 genomes
AF:
0.0234
AC:
3563
AN:
152176
Hom.:
338
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00705
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0671
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.290
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.00264
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00106
Gnomad OTH
AF:
0.0230
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0234
AC:
3561
AN:
152294
Hom.:
337
Cov.:
33
AF XY:
0.0279
AC XY:
2079
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.00703
Gnomad4 AMR
AF:
0.0672
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.289
Gnomad4 SAS
AF:
0.122
Gnomad4 FIN
AF:
0.00264
Gnomad4 NFE
AF:
0.00106
Gnomad4 OTH
AF:
0.0227
Alfa
AF:
0.0109
Hom.:
15
Bravo
AF:
0.0292
Asia WGS
AF:
0.158
AC:
550
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.52

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs5743947; hg19: chr11-1313664; API