17-2597742-TTCTC-T

Variant summary

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

The NM_000430.4(PAFAH1B1):​c.-191+3741_-191+3744del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6171 hom., cov: 15)

Consequence

PAFAH1B1
NM_000430.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00200
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 17-2597742-TTCTC-T is Benign according to our data. Variant chr17-2597742-TTCTC-T is described in ClinVar as [Benign]. Clinvar id is 1183503.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAFAH1B1NM_000430.4 linkuse as main transcriptc.-191+3741_-191+3744del intron_variant ENST00000397195.10 NP_000421.1
PAFAH1B1XM_011523901.3 linkuse as main transcriptc.-191+3741_-191+3744del intron_variant XP_011522203.1
PAFAH1B1XM_011523902.4 linkuse as main transcriptc.-396+3353_-396+3356del intron_variant XP_011522204.1
PAFAH1B1XM_017024701.2 linkuse as main transcriptc.-191+4417_-191+4420del intron_variant XP_016880190.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PAFAH1B1ENST00000397195.10 linkuse as main transcriptc.-191+3741_-191+3744del intron_variant 1 NM_000430.4 ENSP00000380378 P1P43034-1

Frequencies

GnomAD3 genomes
AF:
0.283
AC:
42706
AN:
151162
Hom.:
6169
Cov.:
15
show subpopulations
Gnomad AFR
AF:
0.269
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.238
Gnomad ASJ
AF:
0.278
Gnomad EAS
AF:
0.119
Gnomad SAS
AF:
0.225
Gnomad FIN
AF:
0.269
Gnomad MID
AF:
0.339
Gnomad NFE
AF:
0.319
Gnomad OTH
AF:
0.256
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.282
AC:
42718
AN:
151280
Hom.:
6171
Cov.:
15
AF XY:
0.275
AC XY:
20346
AN XY:
73862
show subpopulations
Gnomad4 AFR
AF:
0.268
Gnomad4 AMR
AF:
0.238
Gnomad4 ASJ
AF:
0.278
Gnomad4 EAS
AF:
0.119
Gnomad4 SAS
AF:
0.226
Gnomad4 FIN
AF:
0.269
Gnomad4 NFE
AF:
0.319
Gnomad4 OTH
AF:
0.252
Alfa
AF:
0.302
Hom.:
838
Bravo
AF:
0.280
Asia WGS
AF:
0.167
AC:
583
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 14, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10606544; hg19: chr17-2501036; API