1-156581549-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001105669.4(TTC24):​c.185C>T​(p.Ala62Val) variant causes a missense change. The variant allele was found at a frequency of 0.000219 in 1,551,176 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00023 ( 0 hom. )

Consequence

TTC24
NM_001105669.4 missense

Scores

2
12
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.35
Variant links:
Genes affected
TTC24 (HGNC:32348): (tetratricopeptide repeat domain 24)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TTC24NM_001105669.4 linkuse as main transcriptc.185C>T p.Ala62Val missense_variant 2/11 ENST00000368236.8 NP_001099139.2 A2A3L6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TTC24ENST00000368236.8 linkuse as main transcriptc.185C>T p.Ala62Val missense_variant 2/115 NM_001105669.4 ENSP00000357219.3 A2A3L6

Frequencies

GnomAD3 genomes
AF:
0.0000788
AC:
12
AN:
152252
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000723
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:
0.000132
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000131
AC:
20
AN:
152664
Hom.:
0
AF XY:
0.000136
AC XY:
11
AN XY:
81172
show subpopulations
Gnomad AFR exome
AF:
0.000126
Gnomad AMR exome
AF:
0.00
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:
0.000313
Gnomad OTH exome
AF:
0.000230
GnomAD4 exome
AF:
0.000234
AC:
328
AN:
1398924
Hom.:
0
Cov.:
30
AF XY:
0.000236
AC XY:
163
AN XY:
689938
show subpopulations
Gnomad4 AFR exome
AF:
0.0000634
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:
0.000290
Gnomad4 OTH exome
AF:
0.000224
GnomAD4 genome
AF:
0.0000788
AC:
12
AN:
152252
Hom.:
0
Cov.:
33
AF XY:
0.0000134
AC XY:
1
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0000723
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:
0.000132
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000134
Hom.:
0
Bravo
AF:
0.000125
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1

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 submitterclinical testingAmbry GeneticsSep 29, 2022The c.185C>T (p.A62V) alteration is located in exon 2 (coding exon 1) of the TTC24 gene. This alteration results from a C to T substitution at nucleotide position 185, causing the alanine (A) at amino acid position 62 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
Pathogenic
0.64
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.036
T;T
Eigen
Uncertain
0.28
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.70
T;.
M_CAP
Uncertain
0.19
D
MetaRNN
Uncertain
0.73
D;D
MetaSVM
Uncertain
-0.16
T
MutationAssessor
Uncertain
2.4
M;M
MutationTaster
Benign
0.53
N;N
PrimateAI
Uncertain
0.50
T
PROVEAN
Uncertain
-2.8
D;D
REVEL
Uncertain
0.58
Sift
Uncertain
0.0050
D;D
Sift4G
Pathogenic
0.0
D;D
Vest4
0.76
MVP
0.64
MPC
0.48
ClinPred
0.29
T
GERP RS
4.4
Varity_R
0.28
gMVP
0.58

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: rs764108909; hg19: chr1-156551341; API