19-46595170-C-T

Variant names:

• chr19-46595170-C-T
• rs7260181
• ENST00000414155.5:n.318+5713G>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+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: ENSG00000291145 ENST00000414155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.616 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP5D1P	NR_172902.1		n.34+5713G>A		intron	N/A
	PPP5D1P	NR_172903.1		n.34+5713G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291145	ENST00000414155.5	TSL:2	n.318+5713G>A		intron	N/A
	ENSG00000291145	ENST00000593359.3	TSL:3	n.108+5713G>A		intron	N/A
	ENSG00000291145	ENST00000593888.4	TSL:3	n.86-5492G>A		intron	N/A

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

African (AFR) AF: 0.576 AC: 23884 AN: 41466

American (AMR) AF: 0.504 AC: 7699 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2835 AN: 5166

South Asian (SAS) AF: 0.634 AC: 3058 AN: 4820

European-Finnish (FIN) AF: 0.598 AC: 6319 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37018 AN: 67970

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.94
PhyloP100		-1.8
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7260181;

hg19: chr19-47098427;