5-34840722-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_144725.4(TTC23L):āc.51G>Cā(p.Trp17Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000889 in 1,461,640 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.0000089 ( 0 hom. )
Consequence
TTC23L
NM_144725.4 missense
NM_144725.4 missense
Scores
4
8
7
Clinical Significance
Conservation
PhyloP100: 4.69
Genes affected
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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 | UniProt |
---|---|---|---|---|---|---|---|
TTC23L | NM_144725.4 | c.51G>C | p.Trp17Cys | missense_variant | 2/11 | ENST00000505624.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC23L | ENST00000505624.6 | c.51G>C | p.Trp17Cys | missense_variant | 2/11 | 1 | NM_144725.4 | A2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
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31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249158Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135186
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461640Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727100
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GnomAD4 genome Cov.: 31
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31
Bravo
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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 submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.51G>C (p.W17C) alteration is located in exon 2 (coding exon 1) of the TTC23L gene. This alteration results from a G to C substitution at nucleotide position 51, causing the tryptophan (W) at amino acid position 17 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M;.
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.;.;.
REVEL
Benign
Sift
Pathogenic
D;.;.;.
Sift4G
Pathogenic
D;.;D;.
Polyphen
D;.;.;.
Vest4
MutPred
Gain of disorder (P = 0.0165);Gain of disorder (P = 0.0165);Gain of disorder (P = 0.0165);Gain of disorder (P = 0.0165);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at