5-34845636-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144725.4(TTC23L):c.218C>T(p.Ser73Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,460,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S73Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_144725.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC23L | NM_144725.4 | c.218C>T | p.Ser73Phe | missense_variant | 3/11 | ENST00000505624.6 | |
LOC124900959 | XR_007058729.1 | n.582-2530G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC23L | ENST00000505624.6 | c.218C>T | p.Ser73Phe | missense_variant | 3/11 | 1 | NM_144725.4 | A2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247702Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134380
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460834Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726650
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.218C>T (p.S73F) alteration is located in exon 3 (coding exon 2) of the TTC23L gene. This alteration results from a C to T substitution at nucleotide position 218, causing the serine (S) at amino acid position 73 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at