chr20-5302393-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_144773.4(PROKR2):c.802C>T(p.Arg268Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,614,202 control chromosomes in the GnomAD database, including 108 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R268H) has been classified as Uncertain significance.
Frequency
Consequence
NM_144773.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROKR2 | NM_144773.4 | c.802C>T | p.Arg268Cys | missense_variant | 3/3 | ENST00000678254.1 | |
PROKR2 | XM_017027646.2 | c.802C>T | p.Arg268Cys | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROKR2 | ENST00000678254.1 | c.802C>T | p.Arg268Cys | missense_variant | 3/3 | NM_144773.4 | P1 | ||
PROKR2 | ENST00000217270.4 | c.802C>T | p.Arg268Cys | missense_variant | 3/3 | 1 | P1 | ||
PROKR2 | ENST00000678059.1 | c.694C>T | p.Arg232Cys | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0132 AC: 2007AN: 152206Hom.: 52 Cov.: 33
GnomAD3 exomes AF: 0.00391 AC: 983AN: 251350Hom.: 19 AF XY: 0.00305 AC XY: 415AN XY: 135874
GnomAD4 exome AF: 0.00174 AC: 2540AN: 1461878Hom.: 56 Cov.: 32 AF XY: 0.00154 AC XY: 1123AN XY: 727238
GnomAD4 genome AF: 0.0132 AC: 2010AN: 152324Hom.: 52 Cov.: 33 AF XY: 0.0130 AC XY: 969AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 15, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 02, 2018 | - - |
Hypogonadotropic hypogonadism 3 with or without anosmia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at