rs3733868
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003314.3(TTC1):c.746-2484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,316 control chromosomes in the GnomAD database, including 316 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 0.056 ( 316 hom., cov: 33)
Consequence
TTC1
NM_003314.3 intron
NM_003314.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.318
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC1 | NM_003314.3 | c.746-2484C>T | intron_variant | ENST00000231238.10 | |||
TTC1 | NM_001282500.2 | c.746-2484C>T | intron_variant | ||||
PWWP2A | XM_011534424.4 | c.1566+1209G>A | intron_variant | ||||
PWWP2A | XR_007058578.1 | n.1743+1094G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC1 | ENST00000231238.10 | c.746-2484C>T | intron_variant | 1 | NM_003314.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0558 AC: 8491AN: 152196Hom.: 316 Cov.: 33
GnomAD3 genomes
?
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152196
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0557 AC: 8483AN: 152316Hom.: 316 Cov.: 33 AF XY: 0.0585 AC XY: 4353AN XY: 74472
GnomAD4 genome
?
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8483
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152316
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33
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4353
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74472
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Asia WGS
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451
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at