dbSNP rs368187613: TRIM17:p.Val391Leu (chr1-228408464-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_016102.4(TRIM17):c.1171G>T(p.Val391Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 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 the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

TRIM17
NM_016102.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.419

Publications

0 publications found

Variant links:

Genes affected

TRIM17 (HGNC:13430): (tripartite motif containing 17) 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 cytoplasmic bodies. The protein is expressed almost exclusively in the testis, but its function is unknown. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

TRIM17 links:

ENSG00000231563 (HGNC:):

ENSG00000231563 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.055895388).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016102.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM17	NM_016102.4	MANE Select	c.1171G>T	p.Val391Leu	missense	Exon 7 of 7	NP_057186.1	Q9Y577-1
TRIM17	NM_001024940.3		c.1171G>T	p.Val391Leu	missense	Exon 7 of 7	NP_001020111.1	Q9Y577-1
TRIM17	NM_001438323.1		c.1090G>T	p.Val364Leu	missense	Exon 7 of 7	NP_001425252.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM17	ENST00000366698.7	TSL:1 MANE Select	c.1171G>T	p.Val391Leu	missense	Exon 7 of 7	ENSP00000355659.2	Q9Y577-1
TRIM17	ENST00000295033.7	TSL:1	c.1171G>T	p.Val391Leu	missense	Exon 7 of 7	ENSP00000295033.3	Q9Y577-1
TRIM17	ENST00000366697.6	TSL:2	c.1171G>T	p.Val391Leu	missense	Exon 6 of 6	ENSP00000355658.2	Q9Y577-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251414

AF XY:

0.00000736

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000879

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.073

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.78

DEOGEN2

Benign

0.096

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.20

M_CAP

Benign

0.0056

MetaRNN

Benign

0.056

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.12

PhyloP100

-0.42

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.15

REVEL

Benign

0.040

Sift

Benign

0.90

Sift4G

Benign

1.0

Polyphen

0.12

Vest4

0.19

MutPred

0.45

Loss of methylation at K395 (P = 0.0741)

MVP

0.42

MPC

0.25

ClinPred

0.073

GERP RS

1.6

Varity_R

0.081

gMVP

0.35

Mutation Taster

=95/5

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over