rs2107195

Variant summary

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

The NM_033229.3(TRIM15):​c.732-412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,066 control chromosomes in the GnomAD database, including 2,262 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 0.16 ( 2262 hom., cov: 31)

Consequence

TRIM15
NM_033229.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.72
Variant links:
Genes affected
TRIM15 (HGNC:16284): (tripartite motif containing 15) 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 localizes to the cytoplasm. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRIM15NM_033229.3 linkuse as main transcriptc.732-412A>G intron_variant ENST00000376694.9 NP_150232.2
TRIM15XM_011514987.2 linkuse as main transcriptc.417-412A>G intron_variant XP_011513289.1
TRIM15XM_011514988.3 linkuse as main transcriptc.111-412A>G intron_variant XP_011513290.1
TRIM15XM_047419503.1 linkuse as main transcriptc.718-412A>G intron_variant XP_047275459.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRIM15ENST00000376694.9 linkuse as main transcriptc.732-412A>G intron_variant 1 NM_033229.3 ENSP00000365884 P1Q9C019-1
TRIM15ENST00000433744.1 linkuse as main transcriptc.242-412A>G intron_variant 3 ENSP00000398285
TRIM15ENST00000619857.4 linkuse as main transcriptc.524+237A>G intron_variant 5 ENSP00000484001

Frequencies

GnomAD3 genomes
AF:
0.158
AC:
24013
AN:
151948
Hom.:
2261
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.117
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.215
Gnomad EAS
AF:
0.0520
Gnomad SAS
AF:
0.204
Gnomad FIN
AF:
0.0360
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.123
Gnomad OTH
AF:
0.183
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.158
AC:
24048
AN:
152066
Hom.:
2262
Cov.:
31
AF XY:
0.156
AC XY:
11567
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.253
Gnomad4 AMR
AF:
0.148
Gnomad4 ASJ
AF:
0.215
Gnomad4 EAS
AF:
0.0523
Gnomad4 SAS
AF:
0.204
Gnomad4 FIN
AF:
0.0360
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.180
Alfa
AF:
0.150
Hom.:
565
Bravo
AF:
0.173
Asia WGS
AF:
0.118
AC:
415
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.039
DANN
Benign
0.51

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: rs2107195; hg19: chr6-30137866; API