10-94132372-T-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_016341.4(PLCE1):c.1405T>A(p.Ser469Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 1,613,938 control chromosomes in the GnomAD database, including 1,176 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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.1405T>A | p.Ser469Thr | missense_variant | 3/33 | ENST00000371380.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCE1 | ENST00000371380.8 | c.1405T>A | p.Ser469Thr | missense_variant | 3/33 | 1 | NM_016341.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0295 AC: 4478AN: 152038Hom.: 95 Cov.: 32
GnomAD3 exomes AF: 0.0311 AC: 7757AN: 249366Hom.: 162 AF XY: 0.0320 AC XY: 4333AN XY: 135262
GnomAD4 exome AF: 0.0359 AC: 52431AN: 1461782Hom.: 1081 Cov.: 32 AF XY: 0.0356 AC XY: 25885AN XY: 727196
GnomAD4 genome AF: 0.0294 AC: 4478AN: 152156Hom.: 95 Cov.: 32 AF XY: 0.0280 AC XY: 2085AN XY: 74416
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 27, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Nephrotic syndrome, type 3 Benign:1
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. - |
Focal segmental glomerulosclerosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 26, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at