chr11-72317186-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_030813.6(CLPB):āc.998A>Gā(p.Glu333Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000596 in 1,612,086 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E333V) has been classified as Uncertain significance.
Frequency
Consequence
NM_030813.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLPB | NM_030813.6 | c.998A>G | p.Glu333Gly | missense_variant | 8/17 | ENST00000294053.9 | |
CLPB | NM_001258392.3 | c.908A>G | p.Glu303Gly | missense_variant | 7/16 | ENST00000538039.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLPB | ENST00000294053.9 | c.998A>G | p.Glu333Gly | missense_variant | 8/17 | 1 | NM_030813.6 | P4 | |
CLPB | ENST00000538039.6 | c.908A>G | p.Glu303Gly | missense_variant | 7/16 | 2 | NM_001258392.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000764 AC: 19AN: 248816Hom.: 0 AF XY: 0.0000743 AC XY: 10AN XY: 134516
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1459886Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 726228
GnomAD4 genome AF: 0.000322 AC: 49AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74420
ClinVar
Submissions by phenotype
3-methylglutaconic aciduria, type VIIB Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 02, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.998A>G (p.E333G) alteration is located in exon 8 (coding exon 8) of the CLPB gene. This alteration results from a A to G substitution at nucleotide position 998, causing the glutamic acid (E) at amino acid position 333 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at