chr11-14878280-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024514.5(CYP2R1):c.1348G>A(p.Gly450Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/23 in silico tools predict a damaging outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_024514.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2R1 | ENST00000334636.10 | c.1348G>A | p.Gly450Arg | missense_variant | Exon 5 of 5 | 1 | NM_024514.5 | ENSP00000334592.5 | ||
CYP2R1 | ENST00000532805.1 | n.*456G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000465097.1 | ||||
CYP2R1 | ENST00000532805.1 | n.*456G>A | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000465097.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460728Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726656
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.