chr1-23814294-T-C
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000191.3(HMGCL):c.393A>G(p.Ser131Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000483 in 1,614,072 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000191.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- 3-hydroxy-3-methylglutaric aciduriaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, Orphanet, Myriad Women’s Health, ClinGen
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00269 AC: 410AN: 152208Hom.: 3 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.000648 AC: 163AN: 251468 AF XY: 0.000449 show subpopulations
GnomAD4 exome AF: 0.000252 AC: 368AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.000224 AC XY: 163AN XY: 727184 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00270 AC: 411AN: 152326Hom.: 3 Cov.: 31 AF XY: 0.00274 AC XY: 204AN XY: 74488 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
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HMGCL: BP4, BP7, BS2 -
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Deficiency of hydroxymethylglutaryl-CoA lyase Benign:2
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Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at