16-20636754-G-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001318890.3(ACSM1):c.1284C>A(p.Leu428=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00512 in 1,613,998 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 26 hom. )
Consequence
ACSM1
NM_001318890.3 synonymous
NM_001318890.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0380
Genes affected
ACSM1 (HGNC:18049): (acyl-CoA synthetase medium chain family member 1) Enables CoA-ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
ACSM3 (HGNC:10522): (acyl-CoA synthetase medium chain family member 3) Enables butyrate-CoA ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrion. Implicated in IgA glomerulonephritis. Biomarker of ulcerative colitis. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 16-20636754-G-T is Benign according to our data. Variant chr16-20636754-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646284.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=0.038 with no splicing effect.
BS2
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High Homozygotes in GnomAdExome4 at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSM1 | NM_001318890.3 | c.1284C>A | p.Leu428= | synonymous_variant | 10/14 | ENST00000520010.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSM1 | ENST00000520010.6 | c.1284C>A | p.Leu428= | synonymous_variant | 10/14 | 1 | NM_001318890.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00345 AC: 525AN: 152212Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00306 AC: 769AN: 251170Hom.: 3 AF XY: 0.00312 AC XY: 423AN XY: 135720
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GnomAD4 exome AF: 0.00530 AC: 7745AN: 1461668Hom.: 26 Cov.: 30 AF XY: 0.00516 AC XY: 3750AN XY: 727138
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GnomAD4 genome ? AF: 0.00345 AC: 525AN: 152330Hom.: 1 Cov.: 32 AF XY: 0.00318 AC XY: 237AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | ACSM1: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at