1-186306353-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_005807.6(PRG4):c.634C>T(p.Pro212Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,606,948 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005807.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRG4 | NM_005807.6 | c.634C>T | p.Pro212Ser | missense_variant | 7/13 | ENST00000445192.7 | NP_005798.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRG4 | ENST00000445192.7 | c.634C>T | p.Pro212Ser | missense_variant | 7/13 | 5 | NM_005807.6 | ENSP00000399679 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 151940Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000524 AC: 129AN: 246142Hom.: 0 AF XY: 0.000715 AC XY: 95AN XY: 132844
GnomAD4 exome AF: 0.000237 AC: 345AN: 1454890Hom.: 2 Cov.: 31 AF XY: 0.000341 AC XY: 247AN XY: 723464
GnomAD4 genome AF: 0.0000921 AC: 14AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
PRG4-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 06, 2022 | 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