chr13-48001557-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000423869.1(SUCLA2-AS1):n.169G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 514,794 control chromosomes in the GnomAD database, including 223,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.94 ( 66703 hom., cov: 34)
Exomes 𝑓: 0.93 ( 157001 hom. )
Consequence
SUCLA2-AS1
ENST00000423869.1 non_coding_transcript_exon
ENST00000423869.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.847
Genes affected
SUCLA2-AS1 (HGNC:39965): (SUCLA2 antisense RNA 1)
SUCLA2 (HGNC:11448): (succinate-CoA ligase ADP-forming subunit beta) Succinyl-CoA synthetase (SCS) is a mitochondrial matrix enzyme that acts as a heterodimer, being composed of an invariant alpha subunit and a substrate-specific beta subunit. The protein encoded by this gene is an ATP-specific SCS beta subunit that dimerizes with the SCS alpha subunit to form SCS-A, an essential component of the tricarboxylic acid cycle. SCS-A hydrolyzes ATP to convert succinate to succinyl-CoA. Defects in this gene are a cause of myopathic mitochondrial DNA depletion syndrome. A pseudogene of this gene has been found on chromosome 6. [provided by RefSeq, Jul 2008]
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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 (BayesDel_noAF=-0.88).
BP6
?
Variant 13-48001557-G-T is Benign according to our data. Variant chr13-48001557-G-T is described in ClinVar as [Benign]. Clinvar id is 684102.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUCLA2-AS1 | ENST00000423869.1 | n.169G>T | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
SUCLA2 | ENST00000643246.1 | c.-84-4534C>A | intron_variant | ||||||
SUCLA2 | ENST00000646804.1 | c.-84-4534C>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.936 AC: 142427AN: 152244Hom.: 66652 Cov.: 34
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GnomAD4 exome AF: 0.930 AC: 337167AN: 362432Hom.: 157001 Cov.: 2 AF XY: 0.926 AC XY: 175448AN XY: 189422
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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 | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at