chr1-186300199-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_005807.6(PRG4):c.185G>A(p.Arg62Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005807.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRG4 | NM_005807.6 | c.185G>A | p.Arg62Lys | missense_variant | 3/13 | ENST00000445192.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRG4 | ENST00000445192.7 | c.185G>A | p.Arg62Lys | missense_variant | 3/13 | 5 | NM_005807.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000966 AC: 147AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251468Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135904
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000591 AC XY: 43AN XY: 727190
GnomAD4 genome ? AF: 0.000965 AC: 147AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000940 AC XY: 70AN XY: 74464
ClinVar
Submissions by phenotype
PRG4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at