10-94279840-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016341.4(PLCE1):c.4724G>C(p.Arg1575Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,611,868 control chromosomes in the GnomAD database, including 158,498 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016341.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.466 AC: 70706AN: 151772Hom.: 16716 Cov.: 32
GnomAD3 exomes AF: 0.436 AC: 108444AN: 248886Hom.: 24218 AF XY: 0.437 AC XY: 59031AN XY: 135000
GnomAD4 exome AF: 0.438 AC: 640177AN: 1459978Hom.: 141765 Cov.: 33 AF XY: 0.439 AC XY: 319187AN XY: 726410
GnomAD4 genome AF: 0.466 AC: 70758AN: 151890Hom.: 16733 Cov.: 32 AF XY: 0.461 AC XY: 34175AN XY: 74192
ClinVar
Submissions by phenotype
Nephrotic syndrome, type 3 Benign:4
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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. -
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not provided Benign:3
This variant is associated with the following publications: (PMID: 23688607, 29083407) -
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not specified Benign:2
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This variant is classified as Benign based on local population frequency. This variant was detected in 54% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 50. Only high quality variants are reported. -
Focal segmental glomerulosclerosis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at