chr11-5689666-A-C

Variant summary

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

The ENST00000412903.1(TRIM5):​c.-61-9428T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,284 control chromosomes in the GnomAD database, including 942 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 0.10 ( 942 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

TRIM5
ENST00000412903.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510
Variant links:
Genes affected
TRIM5 (HGNC:16276): (tripartite motif containing 5) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein forms homo-oligomers via the coilel-coil region and localizes to cytoplasmic bodies. It appears to function as a E3 ubiquitin-ligase and ubiqutinates itself to regulate its subcellular localization. It may play a role in retroviral restriction. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2009]
TRIM22 (HGNC:16379): (tripartite motif containing 22) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein localizes to the cytoplasm and its expression is induced by interferon. The protein is involved in innate immunity against different DNA and RNA viruses. [provided by RefSeq, Oct 2021]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM5ENST00000412903.1 linkuse as main transcriptc.-61-9428T>G intron_variant 1
TRIM5ENST00000380027.5 linkuse as main transcriptc.-440-4272T>G intron_variant 5 Q9C035-4
TRIM22ENST00000460454.2 linkuse as main transcriptn.57A>C non_coding_transcript_exon_variant 1/62

Frequencies

GnomAD3 genomes
AF:
0.0999
AC:
15205
AN:
152166
Hom.:
942
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.0761
Gnomad EAS
AF:
0.297
Gnomad SAS
AF:
0.174
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0711
Gnomad OTH
AF:
0.0813
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.100
AC:
15222
AN:
152284
Hom.:
942
Cov.:
33
AF XY:
0.105
AC XY:
7841
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.105
Gnomad4 AMR
AF:
0.127
Gnomad4 ASJ
AF:
0.0761
Gnomad4 EAS
AF:
0.298
Gnomad4 SAS
AF:
0.174
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.0711
Gnomad4 OTH
AF:
0.0823
Alfa
AF:
0.0838
Hom.:
300
Bravo
AF:
0.101
Asia WGS
AF:
0.246
AC:
853
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
5.6
DANN
Benign
0.60

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: rs2291841; hg19: chr11-5710896; API