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 NM_001256598.2(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
NM_001256598.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256598.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPDPFL	NM_001256597.2	MANE Select	c.233+338A>G	intron	N/A	NP_001243526.1	Q8WWR9-3
PPDPFL	NM_001256598.2		c.*140A>G	3_prime_UTR	Exon 5 of 5	NP_001243527.1	Q8WWR9-1
PPDPFL	NM_001256596.1		c.233+338A>G	intron	N/A	NP_001243525.1	Q8WWR9-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPDPFL	ENST00000303202.8	TSL:1	c.*140A>G	3_prime_UTR	Exon 5 of 5	ENSP00000304926.8	Q8WWR9-1
PPDPFL	ENST00000522267.6	TSL:2 MANE Select	c.233+338A>G	intron	N/A	ENSP00000428773.1	Q8WWR9-3
PPDPFL	ENST00000399653.8	TSL:1	c.233+338A>G	intron	N/A	ENSP00000382561.4	Q8WWR9-2

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over