chr5-160021129-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003314.3(TTC1):c.330+10271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 151,948 control chromosomes in the GnomAD database, including 710 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.084 ( 710 hom., cov: 32)
Consequence
TTC1
NM_003314.3 intron
NM_003314.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.581
Publications
6 publications found
Genes affected
TTC1 (HGNC:12391): (tetratricopeptide repeat domain 1) This gene encodes a protein that belongs to the tetratrico peptide repeat superfamily of proteins. The encoded protein plays a role in protein-protein interactions, and binds to the Galpha subunit of G protein-coupled receptors to activate the Ras signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC1 | NM_003314.3 | c.330+10271C>T | intron_variant | Intron 2 of 7 | ENST00000231238.10 | NP_003305.1 | ||
TTC1 | NM_001282500.2 | c.330+10271C>T | intron_variant | Intron 2 of 7 | NP_001269429.1 | |||
LOC124901124 | XR_007059025.1 | n.4373+2098C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0846 AC: 12845AN: 151832Hom.: 711 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
12845
AN:
151832
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0845 AC: 12839AN: 151948Hom.: 710 Cov.: 32 AF XY: 0.0854 AC XY: 6346AN XY: 74292 show subpopulations
GnomAD4 genome
AF:
AC:
12839
AN:
151948
Hom.:
Cov.:
32
AF XY:
AC XY:
6346
AN XY:
74292
show subpopulations
African (AFR)
AF:
AC:
1689
AN:
41486
American (AMR)
AF:
AC:
2783
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
261
AN:
3468
East Asian (EAS)
AF:
AC:
755
AN:
5170
South Asian (SAS)
AF:
AC:
503
AN:
4812
European-Finnish (FIN)
AF:
AC:
755
AN:
10548
Middle Eastern (MID)
AF:
AC:
29
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5835
AN:
67894
Other (OTH)
AF:
AC:
213
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
582
1164
1745
2327
2909
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
150
300
450
600
750
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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