19-46584982-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_172902.1(PPP5D1P):n.34+15901G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,136 control chromosomes in the GnomAD database, including 64,288 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 0.92 (64288 hom., cov: 29)
• Consequence: PPP5D1P NR_172902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP5D1P	NR_172902.1	n.34+15901G>A		intron_variant, non_coding_transcript_variant
PPP5D1P	NR_172903.1	n.34+15901G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP5D1P	ENST00000602017.7	n.107+15901G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139649 AN: 152018 Hom.: 64227 Cov.: 29

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.919 AC: 139769 AN: 152136 Hom.: 64288 Cov.: 29 AF XY: 0.921 AC XY: 68550 AN XY: 74400

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.920

Alfa AF: 0.864 Hom.: 2728

Bravo AF: 0.922

Asia WGS AF: 0.980 AC: 3407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.9
Dann	Benign	0.68

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

Other links and lift over

dbSNP: rs11083838; hg19: chr19-47088239;