17-2593862-C-CCCCGGG
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_000430.4(PAFAH1B1):c.-325_-320dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 145,526 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00035 ( 1 hom., cov: 25)
Exomes 𝑓: 0.0 ( 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: 1.93
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00035 (51/145526) while in subpopulation SAS AF= 0.004 (18/4502). AF 95% confidence interval is 0.00258. There are 1 homozygotes in gnomad4. There are 26 alleles in male gnomad4 subpopulation. Median coverage is 25. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 51 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAFAH1B1 | NM_000430.4 | c.-325_-320dup | 5_prime_UTR_variant | 1/11 | ENST00000397195.10 | NP_000421.1 | ||
PAFAH1B1 | XM_011523901.3 | c.-325_-320dup | 5_prime_UTR_variant | 1/12 | XP_011522203.1 | |||
PAFAH1B1 | XM_017024701.2 | c.-191+542_-191+547dup | intron_variant | XP_016880190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAFAH1B1 | ENST00000397195.10 | c.-325_-320dup | 5_prime_UTR_variant | 1/11 | 1 | NM_000430.4 | ENSP00000380378 | P1 | ||
PAFAH1B1 | ENST00000576586.5 | c.-191+542_-191+547dup | intron_variant | 4 | ENSP00000461087 | |||||
PAFAH1B1 | ENST00000575477.5 | n.58_63dup | non_coding_transcript_exon_variant | 1/4 | 5 | |||||
PAFAH1B1 | ENST00000676201.1 | n.49+170_49+175dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000351 AC: 51AN: 145420Hom.: 1 Cov.: 25
GnomAD3 genomes
AF:
AC:
51
AN:
145420
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 133552Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 67602
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
133552
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
67602
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000350 AC: 51AN: 145526Hom.: 1 Cov.: 25 AF XY: 0.000366 AC XY: 26AN XY: 71126
GnomAD4 genome
AF:
AC:
51
AN:
145526
Hom.:
Cov.:
25
AF XY:
AC XY:
26
AN XY:
71126
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at