chr20-25013978-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032501.4(ACSS1):c.1435G>A(p.Val479Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00315 in 1,613,688 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 65 hom., cov: 33)
Exomes 𝑓: 0.0019 ( 61 hom. )
Consequence
ACSS1
NM_032501.4 missense
NM_032501.4 missense
Scores
1
13
Clinical Significance
Conservation
PhyloP100: 1.49
Genes affected
ACSS1 (HGNC:16091): (acyl-CoA synthetase short chain family member 1) This gene encodes a mitochondrial acetyl-CoA synthetase enzyme. A similar protein in mice plays an important role in the tricarboxylic acid cycle by catalyzing the conversion of acetate to acetyl CoA. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.01578024).
BP6
Variant 20-25013978-C-T is Benign according to our data. Variant chr20-25013978-C-T is described in ClinVar as [Benign]. Clinvar id is 1258805.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSS1 | NM_032501.4 | c.1435G>A | p.Val479Ile | missense_variant | 9/14 | ENST00000323482.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSS1 | ENST00000323482.9 | c.1435G>A | p.Val479Ile | missense_variant | 9/14 | 1 | NM_032501.4 | P1 | |
ACSS1 | ENST00000432802.6 | c.1435G>A | p.Val479Ile | missense_variant | 9/12 | 2 | |||
ACSS1 | ENST00000537502.5 | c.1072G>A | p.Val358Ile | missense_variant | 8/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 2279AN: 152216Hom.: 64 Cov.: 33
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GnomAD3 exomes AF: 0.00447 AC: 1117AN: 249968Hom.: 17 AF XY: 0.00351 AC XY: 475AN XY: 135254
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GnomAD4 exome AF: 0.00192 AC: 2801AN: 1461354Hom.: 61 Cov.: 31 AF XY: 0.00178 AC XY: 1292AN XY: 726952
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GnomAD4 genome AF: 0.0150 AC: 2286AN: 152334Hom.: 65 Cov.: 33 AF XY: 0.0148 AC XY: 1105AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
REVEL
Benign
Sift4G
Benign
T;T;T
Polyphen
0.92
.;.;P
Vest4
MVP
MPC
0.51
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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