dbSNP rs2292399: PPDPFL:c.*140A>G (chr8-49074671-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000303202.8(PPDPFL):c.*140A>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 0.362 in 1,506,684 control chromosomes in the GnomAD database, including 102,531 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 0.31 ( 8228 hom., cov: 32)

Exomes 𝑓: 0.37 ( 94303 hom. )

Consequence

PPDPFL
ENST00000303202.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.644

Publications

10 publications found

Variant links:

Genes affected

PPDPFL (HGNC:31745): (pancreatic progenitor cell differentiation and proliferation factor like) Predicted to be involved in cell differentiation. [provided by Alliance of Genome Resources, Apr 2022]

PPDPFL 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PPDPFL	NM_001256597.2 link	c.233+338A>G	intron_variant	Intron 4 of 4	ENST00000522267.6	NP_001243526.1	Q8WWR9-3
PPDPFL	NM_001256598.2 link	c.*140A>G	3_prime_UTR_variant	Exon 5 of 5		NP_001243527.1	Q8WWR9-1
PPDPFL	NM_001256596.1 link	c.233+338A>G	intron_variant	Intron 4 of 4		NP_001243525.1	Q8WWR9-3
PPDPFL	NM_001007176.5 link	c.233+338A>G	intron_variant	Intron 4 of 4		NP_001007177.1	Q8WWR9-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PPDPFL	ENST00000303202.8 link	c.*140A>G	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000304926.8	Q8WWR9-1
PPDPFL	ENST00000522267.6 link	c.233+338A>G	intron_variant	Intron 4 of 4	2	NM_001256597.2	ENSP00000428773.1	Q8WWR9-3
PPDPFL	ENST00000399653.8 link	c.233+338A>G	intron_variant	Intron 4 of 4	1		ENSP00000382561.4	Q8WWR9-2
PPDPFL	ENST00000517663.5 link	c.233+338A>G	intron_variant	Intron 4 of 4	5		ENSP00000430392.1	Q8WWR9-3

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47542

AN:

151962

Hom.:

8227

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.335

GnomAD4 exome

AF:

0.368

AC:

497921

AN:

1354606

Hom.:

94303

Cov.:

AF XY:

0.363

AC XY:

241524

AN XY:

665198

show subpopulations

African (AFR)

AF:

0.158

AC:

4885

AN:

30914

American (AMR)

AF:

0.247

AC:

8142

AN:

32964

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

7342

AN:

22856

East Asian (EAS)

AF:

0.342

AC:

12129

AN:

35510

South Asian (SAS)

AF:

0.198

AC:

14567

AN:

73484

European-Finnish (FIN)

AF:

0.437

AC:

14239

AN:

32596

Middle Eastern (MID)

AF:

0.318

AC:

1755

AN:

5514

European-Non Finnish (NFE)

AF:

0.390

AC:

415091

AN:

1064100

Other (OTH)

AF:

0.349

AC:

19771

AN:

56668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

15879

31758

47636

63515

79394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13116

26232

39348

52464

65580

<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:

0.313

AC:

47558

AN:

152078

Hom.:

8228

Cov.:

AF XY:

0.314

AC XY:

23358

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.165

AC:

6850

AN:

41524

American (AMR)

AF:

0.304

AC:

4643

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1120

AN:

3462

East Asian (EAS)

AF:

0.338

AC:

1742

AN:

5160

South Asian (SAS)

AF:

0.203

AC:

978

AN:

4818

European-Finnish (FIN)

AF:

0.455

AC:

4803

AN:

10548

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26276

AN:

67966

Other (OTH)

AF:

0.332

AC:

702

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1630

3259

4889

6518

8148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.357

Hom.:

12985

Bravo

AF:

0.298

Asia WGS

AF:

0.251

AC:

873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.19

(source)

DANN

Benign

0.69

PhyloP100

-0.64

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over