rs886038276
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000282.4(PCCA):c.231+47_231+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 1,586,396 control chromosomes in the GnomAD database, including 7,910 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.093 ( 687 hom., cov: 30)
Exomes 𝑓: 0.095 ( 7223 hom. )
Consequence
PCCA
NM_000282.4 intron
NM_000282.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.24
Genes affected
PCCA (HGNC:8653): (propionyl-CoA carboxylase subunit alpha) The protein encoded by this gene is the alpha subunit of the heterodimeric mitochondrial enzyme Propionyl-CoA carboxylase. PCCA encodes the biotin-binding region of this enzyme. Mutations in either PCCA or PCCB (encoding the beta subunit) lead to an enzyme deficiency resulting in propionic acidemia. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 13-100111929-ATTAT-A is Benign according to our data. Variant chr13-100111929-ATTAT-A is described in ClinVar as [Benign]. Clinvar id is 255735.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-100111929-ATTAT-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCCA | NM_000282.4 | c.231+47_231+50del | intron_variant | ENST00000376285.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCA | ENST00000376285.6 | c.231+47_231+50del | intron_variant | 1 | NM_000282.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0929 AC: 14123AN: 152030Hom.: 684 Cov.: 30
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GnomAD3 exomes AF: 0.0856 AC: 21325AN: 249048Hom.: 1041 AF XY: 0.0891 AC XY: 12029AN XY: 134952
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GnomAD4 exome AF: 0.0953 AC: 136698AN: 1434248Hom.: 7223 AF XY: 0.0958 AC XY: 68548AN XY: 715184
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GnomAD4 genome ? AF: 0.0929 AC: 14134AN: 152148Hom.: 687 Cov.: 30 AF XY: 0.0913 AC XY: 6796AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Propionic acidemia Benign:4
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Benign, criteria provided, single submitter | research | Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital | Jan 01, 2011 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 25, 2019 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 15, 2012 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at