Variant chr11-117171692-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000530272.1(PAFAH1B2):c.482C>T(p.Ser161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00928 in 1,535,014 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0069 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0095 ( 79 hom. )

Consequence

PAFAH1B2
ENST00000530272.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.120

Variant links:

Genes affected

PAFAH1B2 (HGNC:8575): (platelet activating factor acetylhydrolase 1b catalytic subunit 2) Platelet-activating factor acetylhydrolase (PAFAH) inactivates platelet-activating factor (PAF) into acetate and LYSO-PAF. This gene encodes the beta subunit of PAFAH, the other subunits are alpha and gamma. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jan 2014]

PAFAH1B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0031649172).

BP6

Variant 11-117171692-C-T is Benign according to our data. Variant chr11-117171692-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2672484.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
PAFAH1B2	NM_001184746.2 linkuse as main transcript	c.482C>T	p.Ser161Leu	missense_variant	6/7
PAFAH1B2	XM_017017840.2 linkuse as main transcript	c.*3993C>T		3_prime_UTR_variant	6/8
PAFAH1B2	XM_047427042.1 linkuse as main transcript	c.*3993C>T		3_prime_UTR_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	UniProt
PAFAH1B2	ENST00000530272.1 linkuse as main transcript	c.482C>T	p.Ser161Leu	missense_variant	6/7	1	P68402-4
PAFAH1B2	ENST00000529887.6 linkuse as main transcript	c.412-4214C>T		intron_variant		1	P68402-2
PAFAH1B2	ENST00000419197.6 linkuse as main transcript	c.394-3201C>T		intron_variant		2	P68402-3
PAFAH1B2	ENST00000526888.1 linkuse as main transcript	n.111-4214C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00692

AC:

1053

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00229

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00589

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00962

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00634

AC:

853

AN:

134536

Hom.:

AF XY:

0.00635

AC XY:

465

AN XY:

73266

show subpopulations

Gnomad AFR exome

AF:

0.00155

Gnomad AMR exome

AF:

0.00405

Gnomad ASJ exome

AF:

0.00458

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00209

Gnomad FIN exome

AF:

0.00967

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00700

GnomAD4 exome

AF:

0.00955

AC:

13199

AN:

1382778

Hom.:

Cov.:

AF XY:

0.00938

AC XY:

6401

AN XY:

682376

show subpopulations

Gnomad4 AFR exome

AF:

0.00184

Gnomad4 AMR exome

AF:

0.00431

Gnomad4 ASJ exome

AF:

0.00433

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00179

Gnomad4 FIN exome

AF:

0.00915

Gnomad4 NFE exome

AF:

0.0111

Gnomad4 OTH exome

AF:

0.00778

GnomAD4 genome

AF:

0.00692

AC:

1053

AN:

152236

Hom.:

Cov.:

AF XY:

0.00634

AC XY:

472

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.00229

Gnomad4 AMR

AF:

0.00589

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.00962

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.0101

Hom.:

Bravo

AF:

0.00677

TwinsUK

AF:

0.0113

AC:

ALSPAC

AF:

0.0122

AC:

ExAC

AF:

0.00339

AC:

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

PAFAH1B2: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.83

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.38

MetaRNN

Benign

0.0032

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

N;N;N

PROVEAN

Benign

1.9

REVEL

Benign

0.16

Sift

Benign

1.0

Sift4G

Benign

0.95

Vest4

0.11

MVP

0.068

ClinPred

0.0041

GERP RS

-0.025

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over