17-2593327-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000576586.5(PAFAH1B1):c.-194C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 152,462 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 33 hom., cov: 32)
Exomes 𝑓: 0.030 ( 0 hom. )
Consequence
PAFAH1B1
ENST00000576586.5 5_prime_UTR
ENST00000576586.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.202
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 17-2593327-C-T is Benign according to our data. Variant chr17-2593327-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1321740.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0167 (2544/152198) while in subpopulation NFE AF= 0.0259 (1759/68000). AF 95% confidence interval is 0.0249. There are 33 homozygotes in gnomad4. There are 1193 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2544 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B1 | XM_017024701.2 | c.-194C>T | 5_prime_UTR_variant | 1/11 | XP_016880190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAFAH1B1 | ENST00000576586.5 | c.-194C>T | 5_prime_UTR_variant | 1/5 | 4 | ENSP00000461087 |
Frequencies
GnomAD3 genomes AF: 0.0167 AC: 2543AN: 152080Hom.: 33 Cov.: 32
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GnomAD4 exome AF: 0.0303 AC: 8AN: 264Hom.: 0 Cov.: 0 AF XY: 0.0297 AC XY: 6AN XY: 202
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GnomAD4 genome AF: 0.0167 AC: 2544AN: 152198Hom.: 33 Cov.: 32 AF XY: 0.0160 AC XY: 1193AN XY: 74406
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at