11-117166645-A-G

Position:

• chr11-117166645-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002572.4(PAFAH1B2):​c.412-776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,160 control chromosomes in the GnomAD database, including 54,265 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 0.84 (54265 hom., cov: 32)
• Consequence: PAFAH1B2 NM_002572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAFAH1B2	NM_002572.4	c.412-776A>G		intron_variant		ENST00000527958.6	NP_002563.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAFAH1B2	ENST00000527958.6	c.412-776A>G		intron_variant		1	NM_002572.4	ENSP00000435289.1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127702 AN: 152042 Hom.: 54229 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.836

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.840 AC: 127783 AN: 152160 Hom.: 54265 Cov.: 32 AF XY: 0.833 AC XY: 61955 AN XY: 74376

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.828

Alfa AF: 0.865 Hom.: 90872

Bravo AF: 0.840

Asia WGS AF: 0.594 AC: 2069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs7112513; hg19: chr11-117037361;