19-46586828-T-C

Variant names:

• chr19-46586828-T-C
• rs4274528
• ENST00000414155.5:n.318+14055A>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+14055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,248 control chromosomes in the GnomAD database, including 63,317 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 0.91 (63317 hom., cov: 31)
• Consequence: ENSG00000291145 ENST00000414155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 3 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=-1.06).
• 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+14055A>G		intron_variant	Intron 1 of 3
PPP5D1P	NR_172903.1	n.34+14055A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291145	ENST00000414155.5	n.318+14055A>G		intron_variant	Intron 1 of 3	2
ENSG00000291145	ENST00000593359.3	n.108+14055A>G		intron_variant	Intron 1 of 2	3
ENSG00000291145	ENST00000593888.4	n.290+2318A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138675 AN: 152130 Hom.: 63263 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.912 AC: 138788 AN: 152248 Hom.: 63317 Cov.: 31 AF XY: 0.914 AC XY: 68065 AN XY: 74430

African (AFR) AF: 0.930 AC: 38615 AN: 41536

American (AMR) AF: 0.932 AC: 14245 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3206 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5123 AN: 5188

South Asian (SAS) AF: 0.967 AC: 4664 AN: 4824

European-Finnish (FIN) AF: 0.905 AC: 9603 AN: 10612

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

European-Non Finnish (NFE) AF: 0.887 AC: 60351 AN: 68018

Other (OTH) AF: 0.913 AC: 1928 AN: 2112

Alfa AF: 0.898 Hom.: 102027

Bravo AF: 0.914

Asia WGS AF: 0.978 AC: 3394 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.33
PhyloP100		-2.8
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: rs4274528; hg19: chr19-47090085;