19-41203461-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030622.8(CYP2S1):āc.988G>Cā(p.Glu330Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,607,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030622.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2S1 | NM_030622.8 | c.988G>C | p.Glu330Gln | missense_variant | 7/9 | ENST00000310054.9 | |
CYP2S1 | XM_047438711.1 | c.976+2089G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2S1 | ENST00000310054.9 | c.988G>C | p.Glu330Gln | missense_variant | 7/9 | 1 | NM_030622.8 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000291 AC: 7AN: 240492Hom.: 0 AF XY: 0.0000307 AC XY: 4AN XY: 130346
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1455296Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723722
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.988G>C (p.E330Q) alteration is located in exon 7 (coding exon 7) of the CYP2S1 gene. This alteration results from a G to C substitution at nucleotide position 988, causing the glutamic acid (E) at amino acid position 330 to be replaced by a glutamine (Q). 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