rs17721321

chr20-5315432-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.-8-1055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,112 control chromosomes in the GnomAD database, including 3,669 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 0.21 (3669 hom., cov: 32)
• Consequence: PROKR2 NM_144773.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROKR2	NM_144773.4	c.-8-1055C>T		intron_variant		ENST00000678254.1
PROKR2	XM_017027646.2	c.-8-1055C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROKR2	ENST00000678254.1	c.-8-1055C>T		intron_variant			NM_144773.4	P1
PROKR2	ENST00000217270.4	c.-9+908C>T		intron_variant		1		P1
PROKR2	ENST00000678059.1	c.-23+1062C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32328 AN: 151994 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.213 AC: 32346 AN: 152112 Hom.: 3669 Cov.: 32 AF XY: 0.212 AC XY: 15782 AN XY: 74350

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.232

Alfa AF: 0.242 Hom.: 4590

Bravo AF: 0.211

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17721321; hg19: chr20-5296078;