chr20-5302232-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_144773.4(PROKR2):c.963C>T(p.Ile321=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,614,192 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000081 ( 1 hom. )
Consequence
PROKR2
NM_144773.4 synonymous
NM_144773.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.156
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 Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 20-5302232-G-A is Benign according to our data. Variant chr20-5302232-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 699964.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.156 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROKR2 | NM_144773.4 | c.963C>T | p.Ile321= | synonymous_variant | 3/3 | ENST00000678254.1 | |
PROKR2 | XM_017027646.2 | c.963C>T | p.Ile321= | synonymous_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROKR2 | ENST00000678254.1 | c.963C>T | p.Ile321= | synonymous_variant | 3/3 | NM_144773.4 | P1 | ||
PROKR2 | ENST00000217270.4 | c.963C>T | p.Ile321= | synonymous_variant | 3/3 | 1 | P1 | ||
PROKR2 | ENST00000678059.1 | c.855C>T | p.Ile285= | synonymous_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251492Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135920
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GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461892Hom.: 1 Cov.: 32 AF XY: 0.0000949 AC XY: 69AN XY: 727248
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2023 | - - |
Computational scores
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at