19-46579995-T-C

Variant names:

• chr19-46579995-T-C
• rs8103534
• ENST00000414155.5:n.318+20888A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414155.5(ENSG00000291145):​n.318+20888A>G variant causes a intron 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: ENSG00000291145 ENST00000414155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 10 publications found

Genes affected

ENSG00000291145 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414155.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP5D1P	NR_172902.1		n.34+20888A>G		intron	N/A
	PPP5D1P	NR_172903.1		n.34+20888A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291145	ENST00000414155.5	TSL:2	n.318+20888A>G		intron	N/A
	ENSG00000291145	ENST00000593359.3	TSL:3	n.108+20888A>G		intron	N/A
	ENSG00000291145	ENST00000593888.4	TSL:3	n.291-3278A>G		intron	N/A

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

African (AFR) AF: 0.287 AC: 11931 AN: 41500

American (AMR) AF: 0.263 AC: 4019 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1438 AN: 3466

East Asian (EAS) AF: 0.102 AC: 530 AN: 5176

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4828

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10566

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20657 AN: 67948

Other (OTH) AF: 0.301 AC: 635 AN: 2108

Alfa AF: 0.302 Hom.: 30355

Bravo AF: 0.288

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		0.030
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8103534; hg19: chr19-47083252;