rs2241437
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017952.6(PTCD3):c.1543+14T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 1,587,638 control chromosomes in the GnomAD database, including 2,173 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.035 ( 230 hom., cov: 32)
Exomes 𝑓: 0.040 ( 1943 hom. )
Consequence
PTCD3
NM_017952.6 intron
NM_017952.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.144
Genes affected
PTCD3 (HGNC:24717): (pentatricopeptide repeat domain 3) Enables rRNA binding activity and ribosomal small subunit binding activity. Involved in mitochondrial translation. Located in several cellular components, including cytosol; mitochondrion; and nucleoplasm. Implicated in combined oxidative phosphorylation deficiency 51. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCD3 | NM_017952.6 | c.1543+14T>G | intron_variant | ENST00000254630.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCD3 | ENST00000254630.12 | c.1543+14T>G | intron_variant | 1 | NM_017952.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0350 AC: 5323AN: 152232Hom.: 230 Cov.: 32
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GnomAD3 exomes AF: 0.0446 AC: 11199AN: 251010Hom.: 678 AF XY: 0.0439 AC XY: 5955AN XY: 135684
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GnomAD4 exome AF: 0.0400 AC: 57349AN: 1435288Hom.: 1943 Cov.: 30 AF XY: 0.0396 AC XY: 28324AN XY: 715486
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GnomAD4 genome ? AF: 0.0350 AC: 5334AN: 152350Hom.: 230 Cov.: 32 AF XY: 0.0350 AC XY: 2605AN XY: 74500
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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