rs117397004
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000282.4(PCCA):āc.24A>Gā(p.Thr8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000612 in 1,522,960 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T8T) has been classified as Likely benign.
Frequency
Consequence
NM_000282.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCCA | NM_000282.4 | c.24A>G | p.Thr8= | synonymous_variant | 1/24 | ENST00000376285.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCA | ENST00000376285.6 | c.24A>G | p.Thr8= | synonymous_variant | 1/24 | 1 | NM_000282.4 | P1 | |
PCCA | ENST00000376286.8 | c.24A>G | p.Thr8= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000376279.7 | c.24A>G | p.Thr8= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000647303.1 | c.24A>G | p.Thr8= | synonymous_variant, NMD_transcript_variant | 1/21 |
Frequencies
GnomAD3 genomes ? AF: 0.000407 AC: 62AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000391 AC: 54AN: 138140Hom.: 0 AF XY: 0.000373 AC XY: 28AN XY: 74980
GnomAD4 exome AF: 0.000635 AC: 870AN: 1370636Hom.: 17 Cov.: 31 AF XY: 0.000673 AC XY: 454AN XY: 674786
GnomAD4 genome ? AF: 0.000407 AC: 62AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74480
ClinVar
Submissions by phenotype
Propionic acidemia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at