rs56371319

Variant names:

• chr11-117172251-C-A
• rs56371319
• ENST00000530272.1:c.536+505C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530272.1(PAFAH1B2):​c.536+505C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,204 control chromosomes in the GnomAD database, including 2,336 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 0.17 (2336 hom., cov: 28)
• Consequence: PAFAH1B2 ENST00000530272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAFAH1B2	NM_001184746.2	c.536+505C>A		intron_variant	Intron 6 of 6		NP_001171675.1
PAFAH1B2	NM_001184747.2	c.412-3655C>A		intron_variant	Intron 5 of 5		NP_001171676.1
PAFAH1B2	NM_001184748.2	c.394-2642C>A		intron_variant	Intron 5 of 5		NP_001171677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAFAH1B2	ENST00000530272.1	c.536+505C>A		intron_variant	Intron 6 of 6	1		ENSP00000431365.1
PAFAH1B2	ENST00000529887.6	c.412-3655C>A		intron_variant	Intron 5 of 5	1		ENSP00000434951.2
PAFAH1B2	ENST00000419197.6	c.394-2642C>A		intron_variant	Intron 5 of 5	2		ENSP00000388742.2
PAFAH1B2	ENST00000526888.1	n.111-3655C>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25666 AN: 151084 Hom.: 2333 Cov.: 28

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.170 AC: 25698 AN: 151204 Hom.: 2336 Cov.: 28 AF XY: 0.171 AC XY: 12606 AN XY: 73820

African (AFR) AF: 0.208 AC: 8542 AN: 41166

American (AMR) AF: 0.199 AC: 3005 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3466

East Asian (EAS) AF: 0.0698 AC: 359 AN: 5146

South Asian (SAS) AF: 0.162 AC: 772 AN: 4756

European-Finnish (FIN) AF: 0.195 AC: 2020 AN: 10368

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10076 AN: 67866

Other (OTH) AF: 0.153 AC: 322 AN: 2104

Alfa AF: 0.167 Hom.: 285

Bravo AF: 0.175

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.84
DANN	Benign	0.40
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56371319; hg19: chr11-117042967;