rs10485485

chr20-5303734-T-C

Variant summary

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

The NM_144773.4(PROKR2):c.459-998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,992 control chromosomes in the GnomAD database, including 958 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 0.11 (958 hom., cov: 31)
• Consequence: PROKR2 NM_144773.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROKR2	NM_144773.4	c.459-998A>G		intron_variant		ENST00000678254.1
PROKR2	XM_017027646.2	c.459-998A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROKR2	ENST00000678254.1	c.459-998A>G		intron_variant			NM_144773.4	P1
PROKR2	ENST00000217270.4	c.459-998A>G		intron_variant		1		P1
PROKR2	ENST00000678059.1	c.351-998A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16227 AN: 151874 Hom.: 959 Cov.: 31

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.107 AC: 16228 AN: 151992 Hom.: 958 Cov.: 31 AF XY: 0.109 AC XY: 8118 AN XY: 74294

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.108

Alfa AF: 0.118 Hom.: 1259

Bravo AF: 0.0981

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.0
Dann	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485485; hg19: chr20-5284380;