17-2593443-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000576586.5(PAFAH1B1):c.-191+113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 152,882 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 66 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 1 hom. )
Consequence
PAFAH1B1
ENST00000576586.5 intron
ENST00000576586.5 intron
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.0920
Genes affected
PAFAH1B1 (HGNC:8574): (platelet activating factor acetylhydrolase 1b regulatory subunit 1) This locus was identified as encoding a gene that when mutated or lost caused the lissencephaly associated with Miller-Dieker lissencephaly syndrome. This gene encodes the non-catalytic alpha subunit of the intracellular Ib isoform of platelet-activating factor acteylhydrolase, a heterotrimeric enzyme that specifically catalyzes the removal of the acetyl group at the SN-2 position of platelet-activating factor (identified as 1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphorylcholine). Two other isoforms of intracellular platelet-activating factor acetylhydrolase exist: one composed of multiple subunits, the other, a single subunit. In addition, a single-subunit isoform of this enzyme is found in serum. [provided by RefSeq, Apr 2009]
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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=-0.62).
BP6
Variant 17-2593443-C-T is Benign according to our data. Variant chr17-2593443-C-T is described in ClinVar as [Benign]. Clinvar id is 1239981.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0505 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B1 | XM_017024701.2 | c.-191+113C>T | intron_variant | XP_016880190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAFAH1B1 | ENST00000576586.5 | c.-191+113C>T | intron_variant | 4 | ENSP00000461087 |
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 2246AN: 152046Hom.: 66 Cov.: 32
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GnomAD4 exome AF: 0.00276 AC: 2AN: 724Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 442
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GnomAD4 genome AF: 0.0148 AC: 2254AN: 152158Hom.: 66 Cov.: 32 AF XY: 0.0146 AC XY: 1086AN XY: 74374
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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 | May 24, 2021 | - - |
Computational scores
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Benign
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Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at