chr1-70411430-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001902.6(CTH):c.15C>A(p.Asp5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001902.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTH | NM_001902.6 | c.15C>A | p.Asp5Glu | missense_variant | 1/12 | ENST00000370938.8 | |
CTH | NM_001190463.2 | c.15C>A | p.Asp5Glu | missense_variant | 1/11 | ||
CTH | NM_153742.5 | c.15C>A | p.Asp5Glu | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTH | ENST00000370938.8 | c.15C>A | p.Asp5Glu | missense_variant | 1/12 | 1 | NM_001902.6 | P1 | |
CTH | ENST00000346806.2 | c.15C>A | p.Asp5Glu | missense_variant | 1/11 | 1 | |||
CTH | ENST00000411986.6 | c.15C>A | p.Asp5Glu | missense_variant | 1/11 | 2 | |||
CTH | ENST00000464926.1 | n.159C>A | non_coding_transcript_exon_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251486Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135916
GnomAD4 exome AF: 0.000214 AC: 313AN: 1461710Hom.: 0 Cov.: 31 AF XY: 0.000187 AC XY: 136AN XY: 727172
GnomAD4 genome AF: 0.000335 AC: 51AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74474
ClinVar
Submissions by phenotype
Cystathioninuria Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.15C>A (p.D5E) alteration is located in exon 1 (coding exon 1) of the CTH gene. This alteration results from a C to A substitution at nucleotide position 15, causing the aspartic acid (D) at amino acid position 5 to be replaced by a glutamic acid (E). 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