chr22-27982673-C-T

Variant summary

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

The NM_001145418.2(TTC28):​c.6994G>A​(p.Ala2332Thr) 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. 15/20 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)

Consequence

TTC28
NM_001145418.2 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.80
Variant links:
Genes affected
TTC28 (HGNC:29179): (tetratricopeptide repeat domain 28) Enables kinase binding activity. Involved in regulation of mitotic cell cycle. Located in midbody. [provided by Alliance of Genome Resources, Apr 2022]
TTC28-AS1 (HGNC:29336): (TTC28 antisense RNA 1)

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=0.109842926).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TTC28NM_001145418.2 linkc.6994G>A p.Ala2332Thr missense_variant Exon 23 of 23 ENST00000397906.7 NP_001138890.1 Q96AY4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TTC28ENST00000397906.7 linkc.6994G>A p.Ala2332Thr missense_variant Exon 23 of 23 1 NM_001145418.2 ENSP00000381003.2 Q96AY4

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
31

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Nov 21, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.6994G>A (p.A2332T) alteration is located in exon 23 (coding exon 23) of the TTC28 gene. This alteration results from a G to A substitution at nucleotide position 6994, causing the alanine (A) at amino acid position 2332 to be replaced by a threonine (T). 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
0.083
BayesDel_addAF
Benign
-0.064
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
18
DANN
Benign
0.96
DEOGEN2
Benign
0.011
T;T
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.58
FATHMM_MKL
Benign
0.70
D
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.11
T;T
MetaSVM
Benign
-0.42
T
MutationAssessor
Benign
2.0
.;M
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-0.38
.;N
REVEL
Benign
0.18
Sift
Benign
0.090
.;T
Sift4G
Benign
0.44
T;T
Polyphen
0.0010
.;B
Vest4
0.18
MutPred
0.12
.;Gain of glycosylation at A2332 (P = 0.0028);
MVP
0.25
ClinPred
0.30
T
GERP RS
4.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.045
gMVP
0.28

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: chr22-28378661; API