Genetic Variant PAFAH1B2:c.411+121T>C (chr11-117164013-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002572.4(PAFAH1B2):c.411+121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 964,624 control chromosomes in the GnomAD database, including 234,312 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 30985 hom., cov: 32)

Exomes 𝑓: 0.70 ( 203327 hom. )

Consequence

PAFAH1B2
NM_002572.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAFAH1B2	NM_002572.4 link	c.411+121T>C		intron_variant	Intron 5 of 5	ENST00000527958.6	NP_002563.1	P68402-1V9HW44

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAFAH1B2	ENST00000527958.6 link	c.411+121T>C		intron_variant	Intron 5 of 5	1	NM_002572.4	ENSP00000435289.1		P68402-1

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93234

AN:

151914

Hom.:

30983

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.666

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.695

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.760

Gnomad OTH

AF:

0.642

GnomAD4 exome

AF:

0.697

AC:

566512

AN:

812592

Hom.:

203327

Cov.:

AF XY:

0.690

AC XY:

289754

AN XY:

419732

show subpopulations

Gnomad4 AFR exome

AF:

0.363

Gnomad4 AMR exome

AF:

0.667

Gnomad4 ASJ exome

AF:

0.661

Gnomad4 EAS exome

AF:

0.384

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.707

Gnomad4 NFE exome

AF:

0.759

Gnomad4 OTH exome

AF:

0.671

GnomAD4 genome

AF:

0.613

AC:

93257

AN:

152032

Hom.:

30985

Cov.:

AF XY:

0.606

AC XY:

45013

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.374

Gnomad4 AMR

AF:

0.654

Gnomad4 ASJ

AF:

0.666

Gnomad4 EAS

AF:

0.375

Gnomad4 SAS

AF:

0.437

Gnomad4 FIN

AF:

0.695

Gnomad4 NFE

AF:

0.760

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.733

Hom.:

41127

Bravo

AF:

0.604

Asia WGS

AF:

0.408

AC:

1420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.1

DANN

Benign

0.30

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over