Variant chr19-10111519-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020230.7(PPAN):c.*354A>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 0.583 in 661,124 control chromosomes in the GnomAD database, including 113,936 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.56 ( 24108 hom., cov: 32)

Exomes 𝑓: 0.59 ( 89828 hom. )

Consequence

PPAN
NM_020230.7 3_prime_UTR

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.269

Variant links:

Genes affected

PPAN (HGNC:9227): (peter pan homolog) The protein encoded by this gene is an evolutionarily conserved protein similar to yeast SSF1 as well as to the gene product of the Drosophila gene peter pan (ppan). SSF1 is known to be involved in the second step of mRNA splicing. Both SSF1 and ppan are essential for cell growth and proliferation. Exogenous expression of this gene was reported to reduce the anchorage-independent growth of some tumor cells. Read-through transcription of this gene with P2RY11/P2Y(11), an adjacent downstream gene that encodes an ATP receptor, has been found. These read-through transcripts are ubiquitously present and up-regulated during granulocyte differentiation. [provided by RefSeq, Nov 2010]

PPAN links:

PPAN-P2RY11 (HGNC:33526): (PPAN-P2RY11 readthrough) This locus represents naturally occurring read-through transcription between the adjacent PPAN and P2RY11 genes. Alternative splicing results in two transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. This transcript is found to be ubiquitously expressed and is up-regulated by agents inducing granulocytic differentiation. However, its functional significance in vivo remains unclear. [provided by RefSeq, Nov 2010]

PPAN-P2RY11 links:

PPAN (HGNC:):

PPAN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPAN	NM_020230.7 linkuse as main transcript	c.*354A>G		3_prime_UTR_variant	12/12	ENST00000253107.12	NP_064615.3	Q9NQ55-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PPAN	ENST00000253107.12 linkuse as main transcript	c.*354A>G	3_prime_UTR_variant	12/12	1	NM_020230.7	ENSP00000253107.7	Q9NQ55-1
PPAN-P2RY11	ENST00000393796.4 linkuse as main transcript	c.1279+497A>G	intron_variant		1		ENSP00000377385.4	A0A0B4J1V8
PPAN-P2RY11	ENST00000428358.5 linkuse as main transcript	c.1341+435A>G	intron_variant		2		ENSP00000411918.1	A0A0A6YYI3
PPAN	ENST00000486482.1 linkuse as main transcript	n.902A>G	non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84557

AN:

151814

Hom.:

24089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.638

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.725

Gnomad SAS

AF:

0.694

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.594

GnomAD4 exome

AF:

0.590

AC:

300603

AN:

509190

Hom.:

89828

Cov.:

AF XY:

0.596

AC XY:

159530

AN XY:

267886

show subpopulations

Gnomad4 AFR exome

AF:

0.471

Gnomad4 AMR exome

AF:

0.679

Gnomad4 ASJ exome

AF:

0.549

Gnomad4 EAS exome

AF:

0.717

Gnomad4 SAS exome

AF:

0.680

Gnomad4 FIN exome

AF:

0.593

Gnomad4 NFE exome

AF:

0.565

Gnomad4 OTH exome

AF:

0.578

GnomAD4 genome

AF:

0.557

AC:

84619

AN:

151934

Hom.:

24108

Cov.:

AF XY:

0.563

AC XY:

41809

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.637

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.726

Gnomad4 SAS

AF:

0.694

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.562

Gnomad4 OTH

AF:

0.596

Alfa

AF:

0.567

Hom.:

24171

Bravo

AF:

0.559

Asia WGS

AF:

0.688

AC:

2391

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Cataplexy and narcolepsy

Other:1

association, no assertion criteria provided

case-control

Center for Narcolepsy, Stanford University

Dec 10, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over