rs151328418
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005518.4(HMGCS2):c.1124C>T(p.Ser375Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S375C) has been classified as Likely benign.
Frequency
Consequence
NM_005518.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMGCS2 | NM_005518.4 | c.1124C>T | p.Ser375Phe | missense_variant | 6/10 | ENST00000369406.8 | |
HMGCS2 | NM_001166107.1 | c.998C>T | p.Ser333Phe | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGCS2 | ENST00000369406.8 | c.1124C>T | p.Ser375Phe | missense_variant | 6/10 | 1 | NM_005518.4 | P1 | |
HMGCS2 | ENST00000544913.2 | c.998C>T | p.Ser333Phe | missense_variant | 5/9 | 2 | |||
HMGCS2 | ENST00000472375.5 | n.571C>T | non_coding_transcript_exon_variant | 3/3 | 5 | ||||
HMGCS2 | ENST00000476640.1 | n.855C>T | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727220
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at