chr20-8788466-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_015192.4(PLCB1):c.3129G>A(p.Thr1043=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,398 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. T1043T) has been classified as Likely benign.
Frequency
Consequence
NM_015192.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCB1 | NM_015192.4 | c.3129G>A | p.Thr1043= | synonymous_variant | 28/32 | ENST00000338037.11 | |
PLCB1 | NM_182734.3 | c.3129G>A | p.Thr1043= | synonymous_variant | 28/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCB1 | ENST00000338037.11 | c.3129G>A | p.Thr1043= | synonymous_variant | 28/32 | 1 | NM_015192.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250204Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135200
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461126Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726794
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74464
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 09, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at