Genetic Variant NM_002572.4:c.*910T>G (chr11-117168609-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.961

Publications

11 publications found

Variant links:

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]

PAFAH1B2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PAFAH1B2	NM_002572.4	MANE Select	c.*910T>G	3_prime_UTR	Exon 6 of 6	NP_002563.1
PAFAH1B2	NR_110282.2		n.1444T>G	non_coding_transcript_exon	Exon 3 of 3
PAFAH1B2	NM_001309431.2		c.*910T>G	3_prime_UTR	Exon 5 of 5	NP_001296360.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PAFAH1B2	ENST00000527958.6	TSL:1 MANE Select	c.*910T>G	3_prime_UTR	Exon 6 of 6	ENSP00000435289.1
PAFAH1B2	ENST00000530272.1	TSL:1	c.412-3013T>G	intron	N/A	ENSP00000431365.1
PAFAH1B2	ENST00000529887.6	TSL:1	c.411+4717T>G	intron	N/A	ENSP00000434951.2

Frequencies

GnomAD3 genomes

AF:

0.841

AC:

127081

AN:

151176

Hom.:

54020

Cov.:

show subpopulations

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.:

AF XY:

0.882

AC XY:

371240

AN XY:

420714

show subpopulations

African (AFR)

AF:

0.833

AC:

16282

AN:

19556

American (AMR)

AF:

0.812

AC:

2767

AN:

3406

Ashkenazi Jewish (ASJ)

AF:

0.830

AC:

8404

AN:

10124

East Asian (EAS)

AF:

0.523

AC:

7707

AN:

14746

South Asian (SAS)

AF:

0.653

AC:

11170

AN:

17110

European-Finnish (FIN)

AF:

0.922

AC:

306

AN:

332

Middle Eastern (MID)

AF:

0.784

AC:

1643

AN:

2096

European-Non Finnish (NFE)

AF:

0.898

AC:

727698

AN:

810104

Other (OTH)

AF:

0.842

AC:

28491

AN:

33838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

4593

9186

13780

18373

22966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20110

40220

60330

80440

100550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.841

AC:

127162

AN:

151292

Hom.:

54057

Cov.:

AF XY:

0.834

AC XY:

61607

AN XY:

73886

show subpopulations

African (AFR)

AF:

0.837

AC:

34493

AN:

41194

American (AMR)

AF:

0.792

AC:

12008

AN:

15160

Ashkenazi Jewish (ASJ)

AF:

0.833

AC:

2890

AN:

3470

East Asian (EAS)

AF:

0.504

AC:

2602

AN:

5162

South Asian (SAS)

AF:

0.643

AC:

3073

AN:

4780

European-Finnish (FIN)

AF:

0.857

AC:

8923

AN:

10410

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.889

AC:

60310

AN:

67822

Other (OTH)

AF:

0.826

AC:

1727

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

906

1812

2718

3624

4530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.862

Hom.:

15075

Bravo

AF:

0.841

Asia WGS

AF:

0.594

AC:

2068

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

0.96

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over