chr10-95064922-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_000770.3(CYP2C8):c.520C>T(p.Pro174Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,611,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000770.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2C8 | NM_000770.3 | c.520C>T | p.Pro174Ser | missense_variant | 4/9 | ENST00000371270.6 | |
CYP2C8 | NM_001198853.1 | c.310C>T | p.Pro104Ser | missense_variant | 4/9 | ||
CYP2C8 | NM_001198855.1 | c.310C>T | p.Pro104Ser | missense_variant | 5/10 | ||
CYP2C8 | NM_001198854.1 | c.214C>T | p.Pro72Ser | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2C8 | ENST00000371270.6 | c.520C>T | p.Pro174Ser | missense_variant | 4/9 | 1 | NM_000770.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251088Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135708
GnomAD4 exome AF: 0.0000459 AC: 67AN: 1459256Hom.: 0 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 725856
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2021 | The c.520C>T (p.P174S) alteration is located in exon 4 (coding exon 4) of the CYP2C8 gene. This alteration results from a C to T substitution at nucleotide position 520, causing the proline (P) at amino acid position 174 to be replaced by a serine (S). 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