chr4-105369463-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_176869.3(PPA2):c.*262A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 397,326 control chromosomes in the GnomAD database, including 2,783 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1201 hom., cov: 32)
Exomes 𝑓: 0.10 ( 1582 hom. )
Consequence
PPA2
NM_176869.3 3_prime_UTR
NM_176869.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.401
Genes affected
PPA2 (HGNC:28883): (inorganic pyrophosphatase 2) The protein encoded by this gene is localized to the mitochondrion, is highly similar to members of the inorganic pyrophosphatase (PPase) family, and contains the signature sequence essential for the catalytic activity of PPase. PPases catalyze the hydrolysis of pyrophosphate to inorganic phosphate, which is important for the phosphate metabolism of cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [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=-1.0).
BP6
?
Variant 4-105369463-T-C is Benign according to our data. Variant chr4-105369463-T-C is described in ClinVar as [Benign]. Clinvar id is 1182538.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPA2 | NM_176869.3 | c.*262A>G | 3_prime_UTR_variant | 12/12 | ENST00000341695.10 | ||
PPA2 | NM_006903.4 | c.*262A>G | 3_prime_UTR_variant | 11/11 | |||
PPA2 | NM_176866.2 | c.*262A>G | 3_prime_UTR_variant | 8/8 | |||
PPA2 | NM_176867.3 | c.*262A>G | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPA2 | ENST00000341695.10 | c.*262A>G | 3_prime_UTR_variant | 12/12 | 1 | NM_176869.3 | P1 | ||
PPA2 | ENST00000348706.9 | c.*262A>G | 3_prime_UTR_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.123 AC: 18630AN: 151994Hom.: 1200 Cov.: 32
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GnomAD4 exome AF: 0.104 AC: 25410AN: 245214Hom.: 1582 Cov.: 0 AF XY: 0.101 AC XY: 13108AN XY: 130314
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GnomAD4 genome ? AF: 0.123 AC: 18642AN: 152112Hom.: 1201 Cov.: 32 AF XY: 0.119 AC XY: 8826AN XY: 74370
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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 | Sep 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at