11-117168609-T-G

Position:

• chr11-117168609-T-G

Variant summary

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

The NM_002572.4(PAFAH1B2):​c.*910T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 1,062,604 control chromosomes in the GnomAD database, including 410,834 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 (54057 hom., cov: 26)
  • Exomes 𝑓: 0.88 (356777 hom.)
• Consequence: PAFAH1B2 NM_002572.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

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=-0.51).
• 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	UniProt
PAFAH1B2	NM_002572.4	c.*910T>G		3_prime_UTR_variant	6/6	ENST00000527958.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAFAH1B2	ENST00000527958.6	c.*910T>G		3_prime_UTR_variant	6/6	1	NM_002572.4	P1

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127081 AN: 151176 Hom.: 54020 Cov.: 26

Gnomad AFR AF: 0.837

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: 0.857

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.834

GnomAD4 exome AF: 0.883 AC: 804468 AN: 911312 Hom.: 356777 Cov.: 30 AF XY: 0.882 AC XY: 371240 AN XY: 420714

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.812

Gnomad4 ASJ exome AF: 0.830

Gnomad4 EAS exome AF: 0.523

Gnomad4 SAS exome AF: 0.653

Gnomad4 FIN exome AF: 0.922

Gnomad4 NFE exome AF: 0.898

Gnomad4 OTH exome AF: 0.842

GnomAD4 genome AF: 0.841 AC: 127162 AN: 151292 Hom.: 54057 Cov.: 26 AF XY: 0.834 AC XY: 61607 AN XY: 73886

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.826

Alfa AF: 0.836 Hom.: 6734

Bravo AF: 0.841

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10892082; hg19: chr11-117039325;