10-94171330-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_016341.4(PLCE1):c.1643G>T(p.Arg548Leu) variant causes a missense change. The variant allele was found at a frequency of 0.175 in 1,613,912 control chromosomes in the GnomAD database, including 26,323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R548C) has been classified as Uncertain significance.
Frequency
Consequence
NM_016341.4 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 |
---|---|---|---|---|---|---|---|
PLCE1 | NM_016341.4 | c.1643G>T | p.Arg548Leu | missense_variant | 4/33 | ENST00000371380.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCE1 | ENST00000371380.8 | c.1643G>T | p.Arg548Leu | missense_variant | 4/33 | 1 | NM_016341.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26145AN: 151978Hom.: 2384 Cov.: 32
GnomAD3 exomes AF: 0.172 AC: 42951AN: 249426Hom.: 4355 AF XY: 0.182 AC XY: 24656AN XY: 135306
GnomAD4 exome AF: 0.176 AC: 256581AN: 1461814Hom.: 23934 Cov.: 34 AF XY: 0.180 AC XY: 130640AN XY: 727214
GnomAD4 genome AF: 0.172 AC: 26162AN: 152098Hom.: 2389 Cov.: 32 AF XY: 0.171 AC XY: 12727AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 21. Only high quality variants are reported. - |
Nephrotic syndrome, type 3 Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2019 | This variant is associated with the following publications: (PMID: 25060053, 31013750) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 20, 2017 | - - |
Focal segmental glomerulosclerosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Sep 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at