rs12420127

Variant names:

• chr11-117164603-A-G
• rs12420127
• NM_002572.4:c.411+711A>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.411+711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 152,270 control chromosomes in the GnomAD database, including 230 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 0.046 (230 hom., cov: 32)
• Consequence: PAFAH1B2 NM_002572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0898 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.411+711A>G		intron	N/A	NP_002563.1	P68402-1
	PAFAH1B2	NM_001184746.2		c.411+711A>G		intron	N/A	NP_001171675.1	P68402-4
	PAFAH1B2	NM_001309431.2		c.267+711A>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.411+711A>G		intron	N/A	ENSP00000435289.1	P68402-1
	PAFAH1B2	ENST00000530272.1	TSL:1	c.411+711A>G		intron	N/A	ENSP00000431365.1	P68402-4
	PAFAH1B2	ENST00000304808.10	TSL:1	c.249+711A>G		intron	N/A	ENSP00000304006.6	J3KNE3

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7040 AN: 152152 Hom.: 230 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0461 AC: 7023 AN: 152270 Hom.: 230 Cov.: 32 AF XY: 0.0472 AC XY: 3513 AN XY: 74452

African (AFR) AF: 0.0113 AC: 468 AN: 41542

American (AMR) AF: 0.0313 AC: 479 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0913 AC: 317 AN: 3472

East Asian (EAS) AF: 0.0891 AC: 463 AN: 5194

South Asian (SAS) AF: 0.0970 AC: 468 AN: 4824

European-Finnish (FIN) AF: 0.0748 AC: 793 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3905 AN: 68012

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0555 Hom.: 80

Bravo AF: 0.0424

Asia WGS AF: 0.0810 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.70
PhyloP100		0.65
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: rs12420127; hg19: chr11-117035319;