chr13-19389783-G-A

Position:

• chr13-19389783-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446672.2(PARP4P2):​n.1825+1918G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0664 in 152,062 control chromosomes in the GnomAD database, including 402 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 0.066 (402 hom., cov: 32)
• Consequence: PARP4P2 ENST00000446672.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

PARP4P2 (HGNC:37760): (poly(ADP-ribose) polymerase family member 4 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARP4P2	ENST00000446672.2	n.1825+1918G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10104 AN: 151944 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0664 AC: 10104 AN: 152062 Hom.: 402 Cov.: 32 AF XY: 0.0674 AC XY: 5007 AN XY: 74310

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.0221 Hom.: 14

Bravo AF: 0.0631

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17080801; hg19: chr13-19963923;