rs767395215
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_144773.4(PROKR2):c.522C>T(p.Ile174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
PROKR2
NM_144773.4 synonymous
NM_144773.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.921
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 20-5302673-G-A is Benign according to our data. Variant chr20-5302673-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 436423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-5302673-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.921 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROKR2 | NM_144773.4 | c.522C>T | p.Ile174= | synonymous_variant | 3/3 | ENST00000678254.1 | |
PROKR2 | XM_017027646.2 | c.522C>T | p.Ile174= | synonymous_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROKR2 | ENST00000678254.1 | c.522C>T | p.Ile174= | synonymous_variant | 3/3 | NM_144773.4 | P1 | ||
PROKR2 | ENST00000217270.4 | c.522C>T | p.Ile174= | synonymous_variant | 3/3 | 1 | P1 | ||
PROKR2 | ENST00000678059.1 | c.414C>T | p.Ile138= | synonymous_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251438Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135886
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461852Hom.: 0 Cov.: 40 AF XY: 0.0000124 AC XY: 9AN XY: 727220
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 01, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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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