chr10-52280910-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_006258.4(PRKG1):c.1525C>T(p.His509Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000866 in 1,613,346 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. H509H) has been classified as Likely benign.
Frequency
Consequence
NM_006258.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKG1 | NM_006258.4 | c.1525C>T | p.His509Tyr | missense_variant | 13/18 | ENST00000373980.11 | |
PRKG1 | NM_001098512.3 | c.1480C>T | p.His494Tyr | missense_variant | 13/18 | ||
PRKG1 | NM_001374781.1 | c.316C>T | p.His106Tyr | missense_variant | 9/14 | ||
PRKG1 | XM_017016413.2 | c.1222C>T | p.His408Tyr | missense_variant | 13/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKG1 | ENST00000373980.11 | c.1525C>T | p.His509Tyr | missense_variant | 13/18 | 1 | NM_006258.4 | ||
PRKG1-AS1 | ENST00000452247.7 | n.461+13005G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 211AN: 151956Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00195 AC: 489AN: 250566Hom.: 3 AF XY: 0.00168 AC XY: 228AN XY: 135402
GnomAD4 exome AF: 0.000812 AC: 1186AN: 1461272Hom.: 13 Cov.: 31 AF XY: 0.000770 AC XY: 560AN XY: 726904
GnomAD4 genome AF: 0.00139 AC: 211AN: 152074Hom.: 1 Cov.: 32 AF XY: 0.00153 AC XY: 114AN XY: 74318
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 21, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 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. - |
Aortic aneurysm, familial thoracic 8 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 27, 2021 | - - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 19, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at