rs318039
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001005473.3(PLCXD3):c.103+34760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 534,398 control chromosomes in the GnomAD database, including 30,616 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 0.37 ( 12554 hom., cov: 32)
Exomes 𝑓: 0.30 ( 18062 hom. )
Consequence
PLCXD3
NM_001005473.3 intron
NM_001005473.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.937
Genes affected
PLCXD3 (HGNC:31822): (phosphatidylinositol specific phospholipase C X domain containing 3) Predicted to enable phosphoric diester hydrolase activity. Predicted to be involved in lipid catabolic process and signal transduction. Predicted to be located in cytoplasm. Predicted to be active in glutamatergic synapse. [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=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCXD3 | NM_001005473.3 | c.103+34760G>A | intron_variant | ENST00000377801.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCXD3 | ENST00000377801.8 | c.103+34760G>A | intron_variant | 1 | NM_001005473.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56887AN: 151964Hom.: 12514 Cov.: 32
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GnomAD3 exomes AF: 0.297 AC: 73137AN: 246514Hom.: 12358 AF XY: 0.299 AC XY: 40069AN XY: 134182
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GnomAD4 exome AF: 0.296 AC: 112977AN: 382316Hom.: 18062 Cov.: 0 AF XY: 0.299 AC XY: 65073AN XY: 217658
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GnomAD4 genome ? AF: 0.375 AC: 56975AN: 152082Hom.: 12554 Cov.: 32 AF XY: 0.367 AC XY: 27321AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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