20-5301912-C-T

Position:

• chr20-5301912-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_144773.4(PROKR2):​c.*128G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 782,230 control chromosomes in the GnomAD database, including 5,938 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1181 hom., cov: 33)
  • Exomes 𝑓: 0.12 (4757 hom.)
• Consequence: PROKR2 NM_144773.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.00

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 20-5301912-C-T is Benign according to our data. Variant chr20-5301912-C-T is described in ClinVar as [Benign]. Clinvar id is 1250628.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PROKR2	NM_144773.4	c.*128G>A		3_prime_UTR_variant	3/3	ENST00000678254.1	NP_658986.1
PROKR2	XM_017027646.2	c.*128G>A		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.*128G>A		3_prime_UTR_variant	3/3		NM_144773.4	ENSP00000504128.1
PROKR2	ENST00000217270	c.*128G>A		3_prime_UTR_variant	3/3	1		ENSP00000217270.3
PROKR2	ENST00000678059	c.*128G>A		3_prime_UTR_variant	3/3			ENSP00000503366.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18280 AN: 152102 Hom.: 1181 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.118 AC: 74528 AN: 630008 Hom.: 4757 AF XY: 0.120 AC XY: 38870 AN XY: 325064

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.164

Gnomad4 EAS exome AF: 0.0407

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.168

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome AF: 0.120 AC: 18297 AN: 152222 Hom.: 1181 Cov.: 33 AF XY: 0.122 AC XY: 9107 AN XY: 74422

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0806

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.120

Alfa AF: 0.120 Hom.: 224

Bravo AF: 0.113

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73071931; hg19: chr20-5282558;