19-46584982-C-T

Variant names:

• chr19-46584982-C-T
• rs11083838
• ENST00000414155.5:n.318+15901G>A

Variant summary

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

The ENST00000414155.5(ENSG00000291145):​n.318+15901G>A variant causes a intron 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: ENSG00000291145 ENST00000414155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 2 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=-0.87).
• 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 rank	MANE	Protein	UniProt
PPP5D1P	NR_172902.1	n.34+15901G>A		intron_variant	Intron 1 of 3
PPP5D1P	NR_172903.1	n.34+15901G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291145	ENST00000414155.5	n.318+15901G>A		intron_variant	Intron 1 of 3	2
ENSG00000291145	ENST00000593359.3	n.108+15901G>A		intron_variant	Intron 1 of 2	3
ENSG00000291145	ENST00000593888.4	n.290+4164G>A		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.956 AC: 39680 AN: 41526

American (AMR) AF: 0.935 AC: 14289 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5127 AN: 5192

South Asian (SAS) AF: 0.966 AC: 4659 AN: 4822

European-Finnish (FIN) AF: 0.905 AC: 9550 AN: 10552

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60293 AN: 67980

Other (OTH) AF: 0.920 AC: 1944 AN: 2112

Alfa AF: 0.873 Hom.: 3081

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
PhyloP100		-0.95
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: rs11083838; hg19: chr19-47088239;