NM_003314.3:c.330+10271C>T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.581

Publications

6 publications found
Variant links:
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]

Genome browser will be placed here

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
TTC1NM_003314.3 linkc.330+10271C>T intron_variant Intron 2 of 7 ENST00000231238.10 NP_003305.1 Q99614
TTC1NM_001282500.2 linkc.330+10271C>T intron_variant Intron 2 of 7 NP_001269429.1 Q99614
LOC124901124XR_007059025.1 linkn.4373+2098C>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TTC1ENST00000231238.10 linkc.330+10271C>T intron_variant Intron 2 of 7 1 NM_003314.3 ENSP00000231238.4 Q99614

Frequencies

GnomAD3 genomes
AF:
0.0846
AC:
12845
AN:
151832
Hom.:
711
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0408
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.0753
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.0716
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.0860
Gnomad OTH
AF:
0.102
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0845
AC:
12839
AN:
151948
Hom.:
710
Cov.:
32
AF XY:
0.0854
AC XY:
6346
AN XY:
74292
show subpopulations
African (AFR)
AF:
0.0407
AC:
1689
AN:
41486
American (AMR)
AF:
0.182
AC:
2783
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.0753
AC:
261
AN:
3468
East Asian (EAS)
AF:
0.146
AC:
755
AN:
5170
South Asian (SAS)
AF:
0.105
AC:
503
AN:
4812
European-Finnish (FIN)
AF:
0.0716
AC:
755
AN:
10548
Middle Eastern (MID)
AF:
0.0986
AC:
29
AN:
294
European-Non Finnish (NFE)
AF:
0.0859
AC:
5835
AN:
67894
Other (OTH)
AF:
0.101
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:
0.0906
Hom.:
2350
Bravo
AF:
0.0933

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.7
DANN
Benign
0.45
PhyloP100
0.58
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2176830; hg19: chr5-159448136; COSMIC: COSV51464282; COSMIC: COSV51464282; API