Variant 6-30171922-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_033229.3(TRIM15):c.971G>A(p.Ser324Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,597,126 control chromosomes in the GnomAD database, including 45,418 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.21 ( 3663 hom., cov: 33)

Exomes 𝑓: 0.24 ( 41755 hom. )

Consequence

TRIM15
NM_033229.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

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]

TRIM15 links:

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 (MetaRNN=0.003719598).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM15	NM_033229.3 linkuse as main transcript	c.971G>A	p.Ser324Asn	missense_variant	7/7	ENST00000376694.9	NP_150232.2	Q9C019-1Q5SRL0
TRIM15	XM_011514987.2 linkuse as main transcript	c.656G>A	p.Ser219Asn	missense_variant	8/8		XP_011513289.1
TRIM15	XM_011514988.3 linkuse as main transcript	c.350G>A	p.Ser117Asn	missense_variant	5/5		XP_011513290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRIM15	ENST00000376694.9 linkuse as main transcript	c.971G>A	p.Ser324Asn	missense_variant	7/7	1	NM_033229.3	ENSP00000365884.4	Q9C019-1
TRIM15	ENST00000619857.4 linkuse as main transcript	c.764G>A	p.Ser255Asn	missense_variant	8/8	5		ENSP00000484001.1	A0A087X199
TRIM15	ENST00000433744.1 linkuse as main transcript	c.456G>A	p.Glu152Glu	synonymous_variant	5/5	3		ENSP00000398285.1	H0Y5R0

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31405

AN:

152128

Hom.:

3661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.171

GnomAD3 exomes

AF:

0.222

AC:

47880

AN:

215908

Hom.:

5744

AF XY:

0.215

AC XY:

25392

AN XY:

118148

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.251

Gnomad ASJ exome

AF:

0.152

Gnomad EAS exome

AF:

0.246

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.316

Gnomad NFE exome

AF:

0.244

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.235

AC:

339549

AN:

1444880

Hom.:

41755

Cov.:

AF XY:

0.231

AC XY:

165473

AN XY:

717314

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.256

Gnomad4 ASJ exome

AF:

0.150

Gnomad4 EAS exome

AF:

0.203

Gnomad4 SAS exome

AF:

0.115

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.249

Gnomad4 OTH exome

AF:

0.209

GnomAD4 genome

AF:

0.206

AC:

31417

AN:

152246

Hom.:

3663

Cov.:

AF XY:

0.209

AC XY:

15530

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.238

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.232

Hom.:

9182

Bravo

AF:

0.195

TwinsUK

AF:

0.255

AC:

946

ALSPAC

AF:

0.259

AC:

997

ESP6500AA

AF:

0.110

AC:

330

ESP6500EA

AF:

0.233

AC:

1263

ExAC

AF:

0.204

AC:

23814

Asia WGS

AF:

0.156

AC:

541

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.87

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.25

DANN

Benign

0.84

DEOGEN2

Benign

0.0028

T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.024

MetaRNN

Benign

0.0037

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.14

.;N

PrimateAI

Benign

0.39

PROVEAN

Benign

1.8

.;N

REVEL

Benign

0.021

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

.;B

Vest4

0.0060

MPC

0.37

ClinPred

0.0000096

GERP RS

0.83

Varity_R

0.041

gMVP

0.026

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over