chr2-210477765-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000430249.7(CPS1):āc.2T>Gā(p.Met1?) variant causes a start lost, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000430249.7 start_lost, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPS1 | NM_001122633.3 | c.-17T>G | splice_region_variant, 5_prime_UTR_variant | 1/39 | |||
CPS1 | NM_001369257.1 | c.-137T>G | splice_region_variant, 5_prime_UTR_variant | 1/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPS1 | ENST00000430249.7 | c.2T>G | p.Met1? | start_lost, splice_region_variant | 1/39 | 1 | |||
CPS1 | ENST00000673510.1 | c.-137T>G | splice_region_variant, 5_prime_UTR_variant | 1/40 | P1 | ||||
CPS1 | ENST00000673630.1 | c.-251T>G | splice_region_variant, 5_prime_UTR_variant | 1/40 | P1 | ||||
CPS1 | ENST00000673711.1 | c.-17T>G | splice_region_variant, 5_prime_UTR_variant | 1/39 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461230Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726882
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Congenital hyperammonemia, type I Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 04, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at