rs7258489

Positions:

• chr19-46599884-C-T

Variant summary

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

The ENST00000594701.1(PPP5D1P):​n.1042G>A 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 0.282 in 152,166 control chromosomes in the GnomAD database, including 6,138 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 0.28 (6137 hom., cov: 32)
  • Exomes 𝑓: 0.35 (1 hom.)
• Consequence: PPP5D1P ENST00000594701.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

PPP5D1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP5D1P	NR_172902.1	n.34+999G>A		intron_variant
PPP5D1P	NR_172903.1	n.34+999G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP5D1P	ENST00000594701.1	n.1042G>A		non_coding_transcript_exon_variant	1/1	6
PPP5D1P	ENST00000414155.5	n.318+999G>A		intron_variant		2
PPP5D1P	ENST00000593359.2	n.49+999G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42940 AN: 152022 Hom.: 6145 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.438 AC XY: 7 AN XY: 16

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.282 AC: 42953 AN: 152140 Hom.: 6137 Cov.: 32 AF XY: 0.283 AC XY: 21019 AN XY: 74374

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.299

Alfa AF: 0.304 Hom.: 4904

Bravo AF: 0.281

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.59

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: rs7258489; hg19: chr19-47103141;