14-37749343-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001310135.5(TTC6):c.2768G>T(p.Arg923Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00119 in 1,491,800 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 1 hom. )
Consequence
TTC6
NM_001310135.5 missense
NM_001310135.5 missense
Scores
2
6
7
Clinical Significance
Conservation
PhyloP100: 3.80
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.01342085).
BP6
Variant 14-37749343-G-T is Benign according to our data. Variant chr14-37749343-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3234156.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC6 | NM_001310135.5 | c.2768G>T | p.Arg923Leu | missense_variant | 13/33 | ENST00000553443.6 | NP_001297064.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC6 | ENST00000553443.6 | c.2768G>T | p.Arg923Leu | missense_variant | 13/33 | 5 | NM_001310135.5 | ENSP00000451131 | P1 | |
TTC6 | ENST00000533625.5 | c.*1062+10188G>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000451566 |
Frequencies
GnomAD3 genomes AF: 0.00110 AC: 168AN: 152144Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00191 AC: 205AN: 107608Hom.: 1 AF XY: 0.00196 AC XY: 115AN XY: 58560
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GnomAD4 exome AF: 0.00120 AC: 1607AN: 1339538Hom.: 1 Cov.: 32 AF XY: 0.00127 AC XY: 833AN XY: 655562
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GnomAD4 genome AF: 0.00110 AC: 168AN: 152262Hom.: 3 Cov.: 33 AF XY: 0.00102 AC XY: 76AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | TTC6: BP4, BS2 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Benign
D
Sift4G
Pathogenic
D
Vest4
MutPred
Gain of catalytic residue at I926 (P = 0);
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MPC
ClinPred
T
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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