Genetic Variant PPP5D1P:n.755A>G (chr19-46600171-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000594701.1(PPP5D1P):n.755A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,066 control chromosomes in the GnomAD database, including 26,605 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 0.59 ( 26596 hom., cov: 31)

Exomes 𝑓: 0.50 ( 9 hom. )

Consequence

PPP5D1P
ENST00000594701.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0210

Variant links:

Genes affected

PPP5D1P (HGNC:):

PPP5D1P links:

PPP5D1P (HGNC:44209): (PPP5 tetratricopeptide repeat domain containing 1, pseudogene)

PPP5D1P 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP5D1P	NR_172902.1 link	n.34+712A>G		intron_variant	Intron 1 of 3
PPP5D1P	NR_172903.1 link	n.34+712A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PPP5D1P	ENST00000594701.1 link	n.755A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
PPP5D1P	ENST00000414155.5 link	n.318+712A>G	intron_variant	Intron 1 of 3	2
PPP5D1P	ENST00000593359.2 link	n.49+712A>G	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89413

AN:

151896

Hom.:

26588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.887

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.621

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.572

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.583

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.393

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.589

AC:

89475

AN:

152012

Hom.:

26596

Cov.:

AF XY:

0.593

AC XY:

44086

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.558

Gnomad4 AMR

AF:

0.649

Gnomad4 ASJ

AF:

0.474

Gnomad4 EAS

AF:

0.886

Gnomad4 SAS

AF:

0.646

Gnomad4 FIN

AF:

0.621

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.576

Alfa

AF:

0.571

Hom.:

40933

Bravo

AF:

0.588

Asia WGS

AF:

0.776

AC:

2700

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.6

DANN

Benign

0.64

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over