rs8103534

Positions:

• chr19-46579995-T-C

Variant summary

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

The NR_172902.1(PPP5D1P):​n.34+20888A>G 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 0.287 in 152,070 control chromosomes in the GnomAD database, including 6,369 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 0.29 (6369 hom., cov: 31)
• Consequence: PPP5D1P NR_172902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP5D1P	NR_172902.1	n.34+20888A>G		intron_variant, non_coding_transcript_variant
PPP5D1P	NR_172903.1	n.34+20888A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP5D1P	ENST00000602017.7	n.107+20888A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43669 AN: 151952 Hom.: 6375 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.287 AC: 43683 AN: 152070 Hom.: 6369 Cov.: 31 AF XY: 0.285 AC XY: 21194 AN XY: 74322

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.301

Alfa AF: 0.304 Hom.: 14823

Bravo AF: 0.288

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.69

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: rs8103534; hg19: chr19-47083252;