17-2593657-C-CGGAGCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000430.4(PAFAH1B1):​c.-534_-529dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 272,760 control chromosomes in the GnomAD database, including 644 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.051 ( 619 hom., cov: 30)
Exomes 𝑓: 0.0030 ( 25 hom. )

Consequence

PAFAH1B1
NM_000430.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.33
Variant links:
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 Benign. Variant got -10 ACMG points.

BP6
Variant 17-2593657-C-CGGAGCT is Benign according to our data. Variant chr17-2593657-C-CGGAGCT is described in ClinVar as [Benign]. Clinvar id is 322244.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAFAH1B1NM_000430.4 linkuse as main transcriptc.-534_-529dup 5_prime_UTR_variant 1/11 ENST00000397195.10 NP_000421.1
PAFAH1B1XM_011523901.3 linkuse as main transcriptc.-534_-529dup 5_prime_UTR_variant 1/12 XP_011522203.1
PAFAH1B1XM_017024701.2 linkuse as main transcriptc.-191+333_-191+338dup intron_variant XP_016880190.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PAFAH1B1ENST00000397195.10 linkuse as main transcriptc.-534_-529dup 5_prime_UTR_variant 1/111 NM_000430.4 ENSP00000380378 P1P43034-1
PAFAH1B1ENST00000576586.5 linkuse as main transcriptc.-191+333_-191+338dup intron_variant 4 ENSP00000461087
PAFAH1B1ENST00000676201.1 linkuse as main transcriptn.10_15dup non_coding_transcript_exon_variant 1/5

Frequencies

GnomAD3 genomes
AF:
0.0510
AC:
7683
AN:
150592
Hom.:
616
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0230
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000392
Gnomad SAS
AF:
0.0316
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0159
Gnomad NFE
AF:
0.000875
Gnomad OTH
AF:
0.0362
GnomAD4 exome
AF:
0.00297
AC:
363
AN:
122062
Hom.:
25
AF XY:
0.00273
AC XY:
186
AN XY:
68068
show subpopulations
Gnomad4 AFR exome
AF:
0.0779
Gnomad4 AMR exome
AF:
0.00613
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0160
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000193
Gnomad4 OTH exome
AF:
0.00610
GnomAD4 genome
AF:
0.0510
AC:
7691
AN:
150698
Hom.:
619
Cov.:
30
AF XY:
0.0496
AC XY:
3653
AN XY:
73622
show subpopulations
Gnomad4 AFR
AF:
0.171
Gnomad4 AMR
AF:
0.0230
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000393
Gnomad4 SAS
AF:
0.0315
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000875
Gnomad4 OTH
AF:
0.0358
Alfa
AF:
0.00833
Hom.:
8
Asia WGS
AF:
0.0180
AC:
61
AN:
3370

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Lissencephaly/Subcortical Band Heterotopia Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs538397985; hg19: chr17-2496951; API