chr17-2595435-T-TTTTTC

Variant summary

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

The NM_000430.4(PAFAH1B1):​c.-191+1431_-191+1432insTTCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 150,950 control chromosomes in the GnomAD database, including 172 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 172 hom., cov: 30)

Consequence

PAFAH1B1
NM_000430.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.516
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 17-2595435-T-TTTTTC is Benign according to our data. Variant chr17-2595435-T-TTTTTC is described in ClinVar as [Benign]. Clinvar id is 1301273.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PAFAH1B1NM_000430.4 linkuse as main transcriptc.-191+1431_-191+1432insTTCTT intron_variant ENST00000397195.10
PAFAH1B1XM_011523901.3 linkuse as main transcriptc.-191+1431_-191+1432insTTCTT intron_variant
PAFAH1B1XM_011523902.4 linkuse as main transcriptc.-396+1043_-396+1044insTTCTT intron_variant
PAFAH1B1XM_017024701.2 linkuse as main transcriptc.-191+2107_-191+2108insTTCTT intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PAFAH1B1ENST00000397195.10 linkuse as main transcriptc.-191+1431_-191+1432insTTCTT intron_variant 1 NM_000430.4 P1P43034-1

Frequencies

GnomAD3 genomes
AF:
0.0216
AC:
3263
AN:
150858
Hom.:
172
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0767
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00646
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.0183
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0217
AC:
3270
AN:
150950
Hom.:
172
Cov.:
30
AF XY:
0.0217
AC XY:
1602
AN XY:
73776
show subpopulations
Gnomad4 AFR
AF:
0.0767
Gnomad4 AMR
AF:
0.00645
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.0181

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 testingGeneDxSep 28, 2021- -

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: rs1188566045; hg19: chr17-2498729; API