rs773120110

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001004342.5(TRIM67):​c.32G>A​(p.Gly11Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G11A) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

TRIM67
NM_001004342.5 missense

Scores

4
10
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.81
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 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.822

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIM67NM_001004342.5 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 10 ENST00000366653.6 NP_001004342.3 Q6ZTA4-3
TRIM67NM_001410937.1 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 10 NP_001397866.1
TRIM67NM_001300889.3 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 12 NP_001287818.1 Q6ZTA4-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM67ENST00000366653.6 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 10 1 NM_001004342.5 ENSP00000355613.5 Q6ZTA4-3
TRIM67ENST00000449018.7 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 12 1 ENSP00000400163.3 Q6ZTA4-2
TRIM67ENST00000444294.7 linkc.32G>A p.Gly11Asp missense_variant Exon 1 of 10 5 ENSP00000412124.3 F8W8C1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460222
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726306
show subpopulations
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.20
D
BayesDel_noAF
Uncertain
0.050
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.26
T;.;T
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Benign
0.25
N
LIST_S2
Uncertain
0.92
D;D;D
M_CAP
Uncertain
0.26
D
MetaRNN
Pathogenic
0.82
D;D;D
MetaSVM
Uncertain
0.045
D
MutationAssessor
Benign
0.87
.;L;L
PrimateAI
Pathogenic
0.88
D
PROVEAN
Benign
-1.7
N;N;N
REVEL
Uncertain
0.62
Sift
Uncertain
0.029
D;T;D
Sift4G
Uncertain
0.015
D;T;D
Polyphen
1.0
.;.;D
Vest4
0.71
MutPred
0.34
Gain of ubiquitination at K6 (P = 0.1008);Gain of ubiquitination at K6 (P = 0.1008);Gain of ubiquitination at K6 (P = 0.1008);
MVP
0.87
MPC
1.8
ClinPred
0.86
D
GERP RS
4.1
Varity_R
0.29
gMVP
0.57

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.

Other links and lift over

hg19: chr1-231298747; API