rs4815785

Positions:

• chr20-5300607-G-A
• chr20-5300607-G-C
• chr20-5300607-G-T

Variant summary

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

The NM_144773.4(PROKR2):​c.*1433C>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 0.731 in 152,094 control chromosomes in the GnomAD database, including 40,654 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 0.73 (40654 hom., cov: 33)
• Consequence: PROKR2 NM_144773.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PROKR2	NM_144773.4	c.*1433C>T		3_prime_UTR_variant	3/3	ENST00000678254.1	NP_658986.1
PROKR2	XM_017027646.2	c.*1433C>T		3_prime_UTR_variant	3/4		XP_016883135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PROKR2	ENST00000678254	c.*1433C>T		3_prime_UTR_variant	3/3		NM_144773.4	ENSP00000504128.1
PROKR2	ENST00000217270	c.*1433C>T		3_prime_UTR_variant	3/3	1		ENSP00000217270.3
PROKR2	ENST00000678059	c.*1433C>T		3_prime_UTR_variant	3/3			ENSP00000503366.1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111133 AN: 151976 Hom.: 40611 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.731 AC: 111226 AN: 152094 Hom.: 40654 Cov.: 33 AF XY: 0.733 AC XY: 54504 AN XY: 74342

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.738

Alfa AF: 0.750 Hom.: 43329

Bravo AF: 0.727

Asia WGS AF: 0.694 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815785; hg19: chr20-5281253;