6-31143055-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001105564.2(CCHCR1):āc.2399A>Gā(p.Lys800Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,612,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001105564.2 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCHCR1 | NM_001105564.2 | c.2399A>G | p.Lys800Arg | missense_variant | 17/18 | ENST00000396268.8 | NP_001099034.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCHCR1 | ENST00000396268.8 | c.2399A>G | p.Lys800Arg | missense_variant | 17/18 | 1 | NM_001105564.2 | ENSP00000379566.3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000608 AC: 15AN: 246592Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134422
GnomAD4 exome AF: 0.000201 AC: 294AN: 1460708Hom.: 0 Cov.: 36 AF XY: 0.000197 AC XY: 143AN XY: 726672
GnomAD4 genome AF: 0.000131 AC: 20AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2024 | The c.2399A>G (p.K800R) alteration is located in exon 17 (coding exon 17) of the CCHCR1 gene. This alteration results from a A to G substitution at nucleotide position 2399, causing the lysine (K) at amino acid position 800 to be replaced by an arginine (R). 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