6-159775264-T-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_005891.3(ACAT2):āc.585T>Gā(p.Ala195=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,614,202 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0054 ( 9 hom., cov: 33)
Exomes š: 0.00055 ( 7 hom. )
Consequence
ACAT2
NM_005891.3 synonymous
NM_005891.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.11
Genes affected
ACAT2 (HGNC:94): (acetyl-CoA acetyltransferase 2) The product of this gene is an enzyme involved in lipid metabolism, and it encodes cytosolic acetoacetyl-CoA thiolase. This gene shows complementary overlapping with the 3-prime region of the TCP1 gene in both mouse and human. These genes are encoded on opposite strands of DNA, as well as in opposite transcriptional orientation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 6-159775264-T-G is Benign according to our data. Variant chr6-159775264-T-G is described in ClinVar as [Benign]. Clinvar id is 781017.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.11 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00542 (825/152340) while in subpopulation AFR AF= 0.0192 (797/41582). AF 95% confidence interval is 0.0181. There are 9 homozygotes in gnomad4. There are 420 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAT2 | NM_005891.3 | c.585T>G | p.Ala195= | synonymous_variant | 5/9 | ENST00000367048.5 | |
ACAT2 | NM_001303253.1 | c.672T>G | p.Ala224= | synonymous_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAT2 | ENST00000367048.5 | c.585T>G | p.Ala195= | synonymous_variant | 5/9 | 1 | NM_005891.3 | P1 | |
ACAT2 | ENST00000467951.1 | n.813T>G | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
ACAT2 | ENST00000472052.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00543 AC: 826AN: 152222Hom.: 10 Cov.: 33
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GnomAD3 exomes AF: 0.00150 AC: 376AN: 251410Hom.: 4 AF XY: 0.00118 AC XY: 160AN XY: 135878
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GnomAD4 exome AF: 0.000553 AC: 808AN: 1461862Hom.: 7 Cov.: 30 AF XY: 0.000484 AC XY: 352AN XY: 727236
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GnomAD4 genome AF: 0.00542 AC: 825AN: 152340Hom.: 9 Cov.: 33 AF XY: 0.00564 AC XY: 420AN XY: 74482
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Aug 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at