chr3-165773388-AC-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PVS1_ModerateBS2_Supporting
The NM_000055.4(BCHE):c.1802delG(p.Gly601ValfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000658 in 1,610,698 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000055.4 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCHE | NM_000055.4 | c.1802delG | p.Gly601ValfsTer4 | frameshift_variant | Exon 4 of 4 | ENST00000264381.8 | NP_000046.1 | |
BCHE | NR_137635.2 | n.395delG | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
BCHE | NR_137636.2 | n.1999delG | non_coding_transcript_exon_variant | Exon 5 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000161 AC: 40AN: 249108Hom.: 1 AF XY: 0.000163 AC XY: 22AN XY: 134638
GnomAD4 exome AF: 0.0000686 AC: 100AN: 1458492Hom.: 2 Cov.: 30 AF XY: 0.0000992 AC XY: 72AN XY: 725636
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: BCHE c.1802delG (p.Gly601ValfsX4) causes a frameshift which results in an extension of the protein. The variant allele was found at a frequency of 0.00016 in 249108 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not significantly higher than estimated for a pathogenic variant in BCHE causing Deficiency Of Butyrylcholine Esterase (0.00016 vs 0.016), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1802delG in individuals affected with Deficiency Of Butyrylcholine Esterase and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at