chr17-2597798-GTC-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000430.4(PAFAH1B1):c.-191+3794_-191+3795del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00304 in 142,158 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 9 hom., cov: 30)
Consequence
PAFAH1B1
NM_000430.4 intron
NM_000430.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.842
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 -10 ACMG points.
BP6
Variant 17-2597798-GTC-G is Benign according to our data. Variant chr17-2597798-GTC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1342740.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00304 (432/142158) while in subpopulation NFE AF= 0.00102 (65/63564). AF 95% confidence interval is 0.000823. There are 9 homozygotes in gnomad4. There are 317 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 432 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAFAH1B1 | NM_000430.4 | c.-191+3794_-191+3795del | intron_variant | ENST00000397195.10 | |||
PAFAH1B1 | XM_011523901.3 | c.-191+3794_-191+3795del | intron_variant | ||||
PAFAH1B1 | XM_011523902.4 | c.-396+3406_-396+3407del | intron_variant | ||||
PAFAH1B1 | XM_017024701.2 | c.-191+4470_-191+4471del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAFAH1B1 | ENST00000397195.10 | c.-191+3794_-191+3795del | intron_variant | 1 | NM_000430.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00304 AC: 432AN: 142038Hom.: 9 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00304 AC: 432AN: 142158Hom.: 9 Cov.: 30 AF XY: 0.00457 AC XY: 317AN XY: 69364
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at