19-46595170-C-T

Variant names:

• chr19-46595170-C-T
• rs7260181
• ENST00000414155.5:n.318+5713G>A

Variant summary

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

The ENST00000414155.5(PPP5D1P):​n.318+5713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,048 control chromosomes in the GnomAD database, including 23,652 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 0.56 (23652 hom., cov: 33)
• Consequence: PPP5D1P ENST00000414155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

PPP5D1P (HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP5D1P	NR_172902.1	n.34+5713G>A		intron_variant	Intron 1 of 3
PPP5D1P	NR_172903.1	n.34+5713G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP5D1P	ENST00000414155.5	n.318+5713G>A		intron_variant	Intron 1 of 3	2
PPP5D1P	ENST00000593359.2	n.49+5713G>A		intron_variant	Intron 1 of 2	3
PPP5D1P	ENST00000593888.4	n.86-5492G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84523 AN: 151930 Hom.: 23634 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.556 AC: 84603 AN: 152048 Hom.: 23652 Cov.: 33 AF XY: 0.560 AC XY: 41643 AN XY: 74324

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.549

Alfa AF: 0.538 Hom.: 3640

Bravo AF: 0.546

Asia WGS AF: 0.592 AC: 2058 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	5.1
DANN	Benign	0.94

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: rs7260181; hg19: chr19-47098427;