5-43294090-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001098272.3(HMGCS1):c.1149G>A(p.Leu383Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,610,592 control chromosomes in the GnomAD database, including 11,220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001098272.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMGCS1 | NM_001098272.3 | c.1149G>A | p.Leu383Leu | synonymous_variant | Exon 8 of 11 | ENST00000325110.11 | NP_001091742.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMGCS1 | ENST00000325110.11 | c.1149G>A | p.Leu383Leu | synonymous_variant | Exon 8 of 11 | 1 | NM_001098272.3 | ENSP00000322706.6 | ||
HMGCS1 | ENST00000433297.2 | c.1149G>A | p.Leu383Leu | synonymous_variant | Exon 7 of 10 | 5 | ENSP00000399402.2 | |||
HMGCS1 | ENST00000508319.1 | n.235G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0866 AC: 13164AN: 151984Hom.: 771 Cov.: 31
GnomAD3 exomes AF: 0.0941 AC: 23654AN: 251278Hom.: 1335 AF XY: 0.0995 AC XY: 13510AN XY: 135806
GnomAD4 exome AF: 0.114 AC: 166496AN: 1458490Hom.: 10454 Cov.: 29 AF XY: 0.114 AC XY: 82887AN XY: 725804
GnomAD4 genome AF: 0.0864 AC: 13148AN: 152102Hom.: 766 Cov.: 31 AF XY: 0.0839 AC XY: 6237AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is associated with the following publications: (PMID: 28171541) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at