rs2992950

Variant names:

• chr13-19354111-A-C
• rs2992950

Variant summary

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

The variant allele was found at a frequency of 0.806 in 152,050 control chromosomes in the GnomAD database, including 51,357 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 0.81 (51357 hom., cov: 31)
• Consequence: PARP4P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP4P2		n.19354111A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP4P2	ENST00000446672.2	n.255+2670A>C		intron_variant	Intron 3 of 20	6

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122563 AN: 151932 Hom.: 51347 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.806 AC: 122616 AN: 152050 Hom.: 51357 Cov.: 31 AF XY: 0.812 AC XY: 60378 AN XY: 74344

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.814

Alfa AF: 0.880 Hom.: 31583

Bravo AF: 0.793

Asia WGS AF: 0.816 AC: 2838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2992950; hg19: chr13-19928251;