rs6516015
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144773.4(PROKR2):c.458+2472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,884 control chromosomes in the GnomAD database, including 20,092 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 0.51 ( 20092 hom., cov: 32)
Consequence
PROKR2
NM_144773.4 intron
NM_144773.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.20
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROKR2 | NM_144773.4 | c.458+2472A>G | intron_variant | ENST00000678254.1 | |||
PROKR2 | XM_017027646.2 | c.458+2472A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROKR2 | ENST00000678254.1 | c.458+2472A>G | intron_variant | NM_144773.4 | P1 | ||||
PROKR2 | ENST00000217270.4 | c.458+2472A>G | intron_variant | 1 | P1 | ||||
PROKR2 | ENST00000678059.1 | c.350+2472A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.510 AC: 77445AN: 151766Hom.: 20056 Cov.: 32
GnomAD3 genomes
?
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77445
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.510 AC: 77535AN: 151884Hom.: 20092 Cov.: 32 AF XY: 0.511 AC XY: 37921AN XY: 74230
GnomAD4 genome
?
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77535
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151884
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32
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37921
AN XY:
74230
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1626
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at