20-9307875-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001377142.1(PLCB4):c.61G>A(p.Ala21Thr) variant causes a missense change. The variant allele was found at a frequency of 0.633 in 1,557,610 control chromosomes in the GnomAD database, including 323,537 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001377142.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLCB4 | NM_001377142.1 | c.61G>A | p.Ala21Thr | missense_variant | Exon 4 of 40 | ENST00000378473.9 | NP_001364071.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCB4 | ENST00000378473.9 | c.61G>A | p.Ala21Thr | missense_variant | Exon 4 of 40 | 1 | NM_001377142.1 | ENSP00000367734.5 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78385AN: 151814Hom.: 23566 Cov.: 31
GnomAD3 exomes AF: 0.596 AC: 147393AN: 247122Hom.: 46298 AF XY: 0.610 AC XY: 81429AN XY: 133598
GnomAD4 exome AF: 0.646 AC: 907575AN: 1405678Hom.: 299964 Cov.: 23 AF XY: 0.648 AC XY: 454891AN XY: 702170
GnomAD4 genome AF: 0.516 AC: 78393AN: 151932Hom.: 23573 Cov.: 31 AF XY: 0.512 AC XY: 38046AN XY: 74250
ClinVar
Submissions by phenotype
Auriculocondylar syndrome 2 Benign:3
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at