11-117153765-T-C

Variant names:

• chr11-117153765-T-C
• rs7940310
• NM_002572.4:c.81+1237T>C

Variant summary

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

The NM_002572.4(PAFAH1B2):​c.81+1237T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 151,982 control chromosomes in the GnomAD database, including 54,096 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 (54096 hom., cov: 30)
• Consequence: PAFAH1B2 NM_002572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 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.81+1237T>C		intron	N/A	NP_002563.1	P68402-1
	PAFAH1B2	NM_001184746.2		c.81+1237T>C		intron	N/A	NP_001171675.1	P68402-4
	PAFAH1B2	NM_001309431.2		c.-63-6169T>C		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.81+1237T>C		intron	N/A	ENSP00000435289.1	P68402-1
	PAFAH1B2	ENST00000530272.1	TSL:1	c.81+1237T>C		intron	N/A	ENSP00000431365.1	P68402-4
	PAFAH1B2	ENST00000304808.10	TSL:1	c.126+9347T>C		intron	N/A	ENSP00000304006.6	J3KNE3

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127430 AN: 151866 Hom.: 54058 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.839 AC: 127513 AN: 151982 Hom.: 54096 Cov.: 30 AF XY: 0.832 AC XY: 61809 AN XY: 74254

African (AFR) AF: 0.832 AC: 34459 AN: 41434

American (AMR) AF: 0.791 AC: 12040 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2891 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2597 AN: 5166

South Asian (SAS) AF: 0.646 AC: 3109 AN: 4816

European-Finnish (FIN) AF: 0.858 AC: 9050 AN: 10550

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

European-Non Finnish (NFE) AF: 0.889 AC: 60486 AN: 68012

Other (OTH) AF: 0.827 AC: 1743 AN: 2108

Alfa AF: 0.824 Hom.: 12813

Bravo AF: 0.839

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.65
PhyloP100		-1.1
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: rs7940310; hg19: chr11-117024481;