1-231163244-C-T

Variant summary

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

The NM_001004342.5(TRIM67):​c.275C>T​(p.Ala92Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TRIM67
NM_001004342.5 missense

Scores

1
1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0200
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]

Genome browser will be placed here

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=0.0947226).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIM67NM_001004342.5 linkc.275C>T p.Ala92Val missense_variant Exon 1 of 10 ENST00000366653.6 NP_001004342.3 Q6ZTA4-3
TRIM67NM_001410937.1 linkc.275C>T p.Ala92Val missense_variant Exon 1 of 10 NP_001397866.1
TRIM67NM_001300889.3 linkc.155C>T p.Ala52Val missense_variant Exon 2 of 12 NP_001287818.1 Q6ZTA4-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM67ENST00000366653.6 linkc.275C>T p.Ala92Val missense_variant Exon 1 of 10 1 NM_001004342.5 ENSP00000355613.5 Q6ZTA4-3
TRIM67ENST00000449018.7 linkc.155C>T p.Ala52Val missense_variant Exon 2 of 12 1 ENSP00000400163.3 Q6ZTA4-2
TRIM67ENST00000444294.7 linkc.275C>T p.Ala92Val missense_variant Exon 1 of 10 5 ENSP00000412124.3 F8W8C1

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152008
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1353408
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
666206
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
AF:
0.00000658
AC:
1
AN:
152008
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 21, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.275C>T (p.A92V) alteration is located in exon 1 (coding exon 1) of the TRIM67 gene. This alteration results from a C to T substitution at nucleotide position 275, causing the alanine (A) at amino acid position 92 to be replaced by a valine (V). 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
0.087
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
17
DANN
Benign
0.97
DEOGEN2
Benign
0.0043
T;.;T
Eigen
Benign
-0.64
Eigen_PC
Benign
-0.57
FATHMM_MKL
Benign
0.043
N
LIST_S2
Benign
0.65
T;T;T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.095
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.20
.;.;N
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-0.46
N;N;N
REVEL
Benign
0.11
Sift
Benign
0.23
T;T;T
Sift4G
Benign
0.16
T;T;T
Polyphen
0.0030
.;.;B
Vest4
0.12
MVP
0.17
MPC
0.71
ClinPred
0.16
T
GERP RS
2.8
Varity_R
0.093
gMVP
0.33

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: rs1175565710; hg19: chr1-231298990; COSMIC: COSV100792003; API