rs4815787

Positions:

• chr20-5301161-G-A

Variant summary

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

The NM_144773.4(PROKR2):​c.*879C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,904 control chromosomes in the GnomAD database, including 15,712 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 0.45 (15712 hom., cov: 32)
• Consequence: PROKR2 NM_144773.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

PROKR2 (HGNC:15836): (prokineticin receptor 2) Prokineticins are secreted proteins that can promote angiogenesis and induce strong gastrointestinal smooth muscle contraction. The protein encoded by this gene is an integral membrane protein and G protein-coupled receptor for prokineticins. The encoded protein is similar in sequence to GPR73, another G protein-coupled receptor for prokineticins. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROKR2	NM_144773.4	c.*879C>T		3_prime_UTR_variant	3/3	ENST00000678254.1
PROKR2	XM_017027646.2	c.*879C>T		3_prime_UTR_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROKR2	ENST00000678254.1	c.*879C>T		3_prime_UTR_variant	3/3		NM_144773.4	P1
PROKR2	ENST00000217270.4	c.*879C>T		3_prime_UTR_variant	3/3	1		P1
PROKR2	ENST00000678059.1	c.*879C>T		3_prime_UTR_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68386 AN: 151786 Hom.: 15698 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.451 AC: 68442 AN: 151904 Hom.: 15712 Cov.: 32 AF XY: 0.452 AC XY: 33554 AN XY: 74244

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.450

Alfa AF: 0.470 Hom.: 2118

Bravo AF: 0.438

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815787; hg19: chr20-5281807;