dbSNP rs20508: PAFAH1B2P2:n.321-44202C>T (chr12-97688809-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000701071.2(PAFAH1B2P2):n.321-44202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,130 control chromosomes in the GnomAD database, including 44,170 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 0.76 ( 44170 hom., cov: 33)

Consequence

PAFAH1B2P2
ENST00000701071.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.959

Publications

5 publications found

Variant links:

Genes affected

PAFAH1B2P2 (HGNC:):

PAFAH1B2P2 links:

Genome browser will be placed here

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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PAFAH1B2P2	ENST00000701071.2 link	n.321-44202C>T	intron_variant	Intron 2 of 2
PAFAH1B2P2	ENST00000847471.1 link	n.316+24895C>T	intron_variant	Intron 3 of 3
PAFAH1B2P2	ENST00000847472.1 link	n.410+30375C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115360

AN:

152012

Hom.:

44123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.858

Gnomad AMI

AF:

0.817

Gnomad AMR

AF:

0.796

Gnomad ASJ

AF:

0.793

Gnomad EAS

AF:

0.590

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.691

Gnomad MID

AF:

0.839

Gnomad NFE

AF:

0.719

Gnomad OTH

AF:

0.773

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

GnomAD4 genome

AF:

0.759

AC:

115466

AN:

152130

Hom.:

44170

Cov.:

AF XY:

0.754

AC XY:

56034

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.858

AC:

35633

AN:

41524

American (AMR)

AF:

0.797

AC:

12165

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.793

AC:

2752

AN:

3472

East Asian (EAS)

AF:

0.590

AC:

3051

AN:

5172

South Asian (SAS)

AF:

0.642

AC:

3099

AN:

4824

European-Finnish (FIN)

AF:

0.691

AC:

7299

AN:

10564

Middle Eastern (MID)

AF:

0.837

AC:

246

AN:

294

European-Non Finnish (NFE)

AF:

0.719

AC:

48847

AN:

67982

Other (OTH)

AF:

0.771

AC:

1629

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1424

2848

4273

5697

7121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.730

Hom.:

20832

Bravo

AF:

0.775

Asia WGS

AF:

0.630

AC:

2193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.8

(source)

DANN

Benign

0.26

PhyloP100

0.96

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over