19-46600171-T-C

Variant names:

• chr19-46600171-T-C
• rs7259810
• ENST00000594701.1:n.755A>G

Variant summary

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

The ENST00000594701.1(ENSG00000291145):​n.755A>G 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 0.589 in 152,066 control chromosomes in the GnomAD database, including 26,605 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 0.59 (26596 hom., cov: 31)
  • Exomes 𝑓: 0.50 (9 hom.)
• Consequence: ENSG00000291145 ENST00000594701.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000594701.1. 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+712A>G		intron	N/A
	PPP5D1P	NR_172903.1		n.34+712A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291145	ENST00000594701.1	TSL:6	n.755A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000291145	ENST00000414155.5	TSL:2	n.318+712A>G		intron	N/A
	ENSG00000291145	ENST00000593359.3	TSL:3	n.108+712A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89413 AN: 151896 Hom.: 26588 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.572

GnomAD4 exome AF: 0.500 AC: 27 AN: 54 Hom.: 9 Cov.: 0 AF XY: 0.583 AC XY: 21 AN XY: 36

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.643 AC: 9 AN: 14

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.393 AC: 11 AN: 28

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.589 AC: 89475 AN: 152012 Hom.: 26596 Cov.: 31 AF XY: 0.593 AC XY: 44086 AN XY: 74290

African (AFR) AF: 0.558 AC: 23120 AN: 41466

American (AMR) AF: 0.649 AC: 9907 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1643 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4581 AN: 5168

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6560 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38625 AN: 67938

Other (OTH) AF: 0.576 AC: 1216 AN: 2112

Alfa AF: 0.574 Hom.: 96606

Bravo AF: 0.588

Asia WGS AF: 0.776 AC: 2700 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	3.6
DANN	Benign	0.64
PhyloP100		-0.021
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: rs7259810;

hg19: chr19-47103428;