Variant chr1-231163856-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 ENST00000366653.6(TRIM67):c.887C>A(p.Thr296Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,408,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

TRIM67
ENST00000366653.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.999

Variant links:

Genes affected

TRIM67 (HGNC:31859): (tripartite motif containing 67) Predicted to enable zinc ion binding activity. Predicted to be involved in regulation of protein localization. Predicted to act upstream of or within negative regulation of Ras protein signal transduction; positive regulation of neuron projection development; and positive regulation of ubiquitin-dependent protein catabolic process. Predicted to be located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

TRIM67 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=0.06982541).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TRIM67	NM_001004342.5 linkuse as main transcript	c.887C>A	p.Thr296Lys	missense_variant	1/10	ENST00000366653.6	NP_001004342.3
TRIM67	NM_001410937.1 linkuse as main transcript	c.887C>A	p.Thr296Lys	missense_variant	1/10		NP_001397866.1
TRIM67	NM_001300889.3 linkuse as main transcript	c.701C>A	p.Thr234Lys	missense_variant	3/12		NP_001287818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM67	ENST00000366653.6 linkuse as main transcript	c.887C>A	p.Thr296Lys	missense_variant	1/10	1	NM_001004342.5	ENSP00000355613	A1	Q6ZTA4-3
TRIM67	ENST00000449018.7 linkuse as main transcript	c.701C>A	p.Thr234Lys	missense_variant	3/12	1		ENSP00000400163		Q6ZTA4-2
TRIM67	ENST00000444294.7 linkuse as main transcript	c.887C>A	p.Thr296Lys	missense_variant	1/10	5		ENSP00000412124	P3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000594

AC:

AN:

168212

Hom.:

AF XY:

0.0000110

AC XY:

AN XY:

90740

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000386

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000142

AC:

AN:

1408816

Hom.:

Cov.:

AF XY:

0.00000287

AC XY:

AN XY:

696032

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000535

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

Feb 17, 2024

The c.887C>A (p.T296K) alteration is located in exon 1 (coding exon 1) of the TRIM67 gene. This alteration results from a C to A substitution at nucleotide position 887, causing the threonine (T) at amino acid position 296 to be replaced by a lysine (K). 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

0.24

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.0055

T;.;T

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.79

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.53

T;T;T

M_CAP

Benign

0.026

MetaRNN

Benign

0.070

T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

.;.;N

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-0.35

N;N;N

REVEL

Benign

0.076

Sift

Uncertain

0.020

D;T;D

Sift4G

Benign

0.10

T;T;T

Polyphen

0.088

.;.;B

Vest4

0.062

MutPred

0.36

Loss of phosphorylation at T296 (P = 0.0057);.;Loss of phosphorylation at T296 (P = 0.0057);

MVP

0.093

MPC

0.71

ClinPred

0.068

GERP RS

2.5

Varity_R

0.17

gMVP

0.36

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over