Variant 1-228406275-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_145214.3(TRIM11):c.287G>T(p.Arg96Leu) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TRIM11
NM_145214.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.331

Variant links:

Genes affected

TRIM11 (HGNC:16281): (tripartite motif containing 11) 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 nucleus and the cytoplasm. Its function has not been identified. [provided by RefSeq, Jul 2008]

TRIM11 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.25173968).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TRIM11	NM_145214.3 linkuse as main transcript	c.287G>T	p.Arg96Leu	missense_variant	1/6	ENST00000284551.11	NP_660215.1
TRIM11	XM_017002412.3 linkuse as main transcript	c.287G>T	p.Arg96Leu	missense_variant	1/6		XP_016857901.1
TRIM11	XM_011544285.4 linkuse as main transcript	c.287G>T	p.Arg96Leu	missense_variant	1/5		XP_011542587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM11	ENST00000284551.11 linkuse as main transcript	c.287G>T	p.Arg96Leu	missense_variant	1/6	1	NM_145214.3	ENSP00000284551	P1	Q96F44-1
TRIM11	ENST00000366699.3 linkuse as main transcript	c.287G>T	p.Arg96Leu	missense_variant	1/5	2		ENSP00000355660		Q96F44-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1341158

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

660464

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 02, 2023

The c.287G>T (p.R96L) alteration is located in exon 1 (coding exon 1) of the TRIM11 gene. This alteration results from a G to T substitution at nucleotide position 287, causing the arginine (R) at amino acid position 96 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

0.00056

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.18

T;.

Eigen

Benign

-0.27

Eigen_PC

Benign

-0.27

FATHMM_MKL

Benign

0.38

LIST_S2

Benign

0.74

T;T

M_CAP

Benign

0.046

MetaRNN

Benign

0.25

T;T

MetaSVM

Benign

-0.80

MutationAssessor

Benign

1.5

L;L

MutationTaster

Benign

0.52

D;D

PrimateAI

Pathogenic

0.85

PROVEAN

Uncertain

-4.1

D;D

REVEL

Benign

0.094

Sift

Benign

0.19

T;T

Sift4G

Benign

0.24

T;T

Polyphen

0.45

B;P

Vest4

0.31

MutPred

0.57

Loss of disorder (P = 0.0689);Loss of disorder (P = 0.0689);

MVP

0.32

MPC

2.7

ClinPred

0.91

GERP RS

2.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Varity_R

0.19

gMVP

0.66

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over