dbSNP rs2992950: PARP4P2:n.19354111A>C (chr13-19354111-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.806 in 152,050 control chromosomes in the GnomAD database, including 51,357 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 0.81 ( 51357 hom., cov: 31)

Consequence

PARP4P2
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.857

Publications

2 publications found

Variant links:

Genes affected

PARP4P2 (HGNC:37760): (poly(ADP-ribose) polymerase family member 4 pseudogene 2)

PARP4P2 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP4P2		n.19354111A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP4P2	ENST00000446672.2 link	n.255+2670A>C		intron_variant	Intron 3 of 20	6

Frequencies

GnomAD3 genomes

AF:

0.807

AC:

122563

AN:

151932

Hom.:

51347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.909

Gnomad AMR

AF:

0.889

Gnomad ASJ

AF:

0.890

Gnomad EAS

AF:

0.907

Gnomad SAS

AF:

0.862

Gnomad FIN

AF:

0.944

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.905

Gnomad OTH

AF:

0.818

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

GnomAD4 genome

AF:

0.806

AC:

122616

AN:

152050

Hom.:

51357

Cov.:

AF XY:

0.812

AC XY:

60378

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.550

AC:

22769

AN:

41410

American (AMR)

AF:

0.889

AC:

13586

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.890

AC:

3085

AN:

3468

East Asian (EAS)

AF:

0.907

AC:

4688

AN:

5168

South Asian (SAS)

AF:

0.862

AC:

4147

AN:

4812

European-Finnish (FIN)

AF:

0.944

AC:

10000

AN:

10598

Middle Eastern (MID)

AF:

0.847

AC:

249

AN:

294

European-Non Finnish (NFE)

AF:

0.905

AC:

61548

AN:

68004

Other (OTH)

AF:

0.814

AC:

1715

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1005

2010

3014

4019

5024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.881

Hom.:

34663

Bravo

AF:

0.793

Asia WGS

AF:

0.816

AC:

2838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.0

(source)

DANN

Benign

0.82

PhyloP100

0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs2992950

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