chr11-117166645-A-G

Variant names:

• chr11-117166645-A-G
• rs7112513
• NM_002572.4:c.412-776A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002572.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAFAH1B2	NM_002572.4	MANE Select	c.412-776A>G		intron	N/A	NP_002563.1	P68402-1
	PAFAH1B2	NM_001184746.2		c.411+2753A>G		intron	N/A	NP_001171675.1	P68402-4
	PAFAH1B2	NM_001309431.2		c.268-776A>G		intron	N/A	NP_001296360.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAFAH1B2	ENST00000527958.6	TSL:1 MANE Select	c.412-776A>G		intron	N/A	ENSP00000435289.1	P68402-1
	PAFAH1B2	ENST00000530272.1	TSL:1	c.411+2753A>G		intron	N/A	ENSP00000431365.1	P68402-4
	PAFAH1B2	ENST00000304808.10	TSL:1	c.250-776A>G		intron	N/A	ENSP00000304006.6	J3KNE3

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

African (AFR) AF: 0.834 AC: 34624 AN: 41494

American (AMR) AF: 0.792 AC: 12105 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2890 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2612 AN: 5182

South Asian (SAS) AF: 0.643 AC: 3101 AN: 4820

European-Finnish (FIN) AF: 0.858 AC: 9072 AN: 10576

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60493 AN: 68014

Other (OTH) AF: 0.828 AC: 1748 AN: 2110

Alfa AF: 0.865 Hom.: 197302

Bravo AF: 0.840

Asia WGS AF: 0.594 AC: 2069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.59
PhyloP100		-0.026
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7112513; hg19: chr11-117037361;