chr1-70411543-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001902.6(CTH):c.128T>C(p.Leu43Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L43L) has been classified as Likely benign.
Frequency
Consequence
NM_001902.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTH | NM_001902.6 | c.128T>C | p.Leu43Pro | missense_variant | 1/12 | ENST00000370938.8 | |
CTH | NM_001190463.2 | c.128T>C | p.Leu43Pro | missense_variant | 1/11 | ||
CTH | NM_153742.5 | c.128T>C | p.Leu43Pro | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTH | ENST00000370938.8 | c.128T>C | p.Leu43Pro | missense_variant | 1/12 | 1 | NM_001902.6 | P1 | |
CTH | ENST00000346806.2 | c.128T>C | p.Leu43Pro | missense_variant | 1/11 | 1 | |||
CTH | ENST00000411986.6 | c.128T>C | p.Leu43Pro | missense_variant | 1/11 | 2 | |||
CTH | ENST00000464926.1 | n.272T>C | non_coding_transcript_exon_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251368Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135880
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727202
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.128T>C (p.L43P) alteration is located in exon 1 (coding exon 1) of the CTH gene. This alteration results from a T to C substitution at nucleotide position 128, causing the leucine (L) at amino acid position 43 to be replaced by a proline (P). 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