17-2593754-GAGA-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000430.4(PAFAH1B1):c.-440_-438del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,734 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PAFAH1B1
NM_000430.4 5_prime_UTR
NM_000430.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.19
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B1 | NM_000430.4 | c.-440_-438del | 5_prime_UTR_variant | 1/11 | ENST00000397195.10 | NP_000421.1 | ||
PAFAH1B1 | XM_011523901.3 | c.-440_-438del | 5_prime_UTR_variant | 1/12 | XP_011522203.1 | |||
PAFAH1B1 | XM_017024701.2 | c.-191+427_-191+429del | intron_variant | XP_016880190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAFAH1B1 | ENST00000397195.10 | c.-440_-438del | 5_prime_UTR_variant | 1/11 | 1 | NM_000430.4 | ENSP00000380378 | P1 | ||
PAFAH1B1 | ENST00000576586.5 | c.-191+427_-191+429del | intron_variant | 4 | ENSP00000461087 | |||||
PAFAH1B1 | ENST00000676201.1 | n.49+55_49+57del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151734Hom.: 0 Cov.: 30
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000431 AC: 1AN: 232016Hom.: 0 AF XY: 0.00000845 AC XY: 1AN XY: 118320
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151734Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74102
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lissencephaly/Subcortical Band Heterotopia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at