3-165773193-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000055.4(BCHE):​c.*189G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 516,674 control chromosomes in the GnomAD database, including 128,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 33343 hom., cov: 31)
Exomes 𝑓: 0.72 ( 94890 hom. )

Consequence

BCHE
NM_000055.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.339
Variant links:
Genes affected
BCHE (HGNC:983): (butyrylcholinesterase) This gene encodes a cholinesterase enzyme and member of the type-B carboxylesterase/lipase family of proteins. The encoded enzyme exhibits broad substrate specificity and is involved in the detoxification of poisons including organophosphate nerve agents and pesticides, and the metabolism of drugs including cocaine, heroin and aspirin. Humans homozygous for certain mutations in this gene exhibit prolonged apnea after administration of the muscle relaxant succinylcholine. [provided by RefSeq, Jul 2016]
LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 3-165773193-C-T is Benign according to our data. Variant chr3-165773193-C-T is described in ClinVar as [Benign]. Clinvar id is 344082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCHENM_000055.4 linkuse as main transcriptc.*189G>A 3_prime_UTR_variant 4/4 ENST00000264381.8
BCHENR_137635.2 linkuse as main transcriptn.591G>A non_coding_transcript_exon_variant 3/3
BCHENR_137636.2 linkuse as main transcriptn.2195G>A non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCHEENST00000264381.8 linkuse as main transcriptc.*189G>A 3_prime_UTR_variant 4/41 NM_000055.4 P1
LINC01322ENST00000651449.1 linkuse as main transcriptn.1008-72699C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.646
AC:
98120
AN:
151792
Hom.:
33324
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.749
Gnomad AMR
AF:
0.754
Gnomad ASJ
AF:
0.679
Gnomad EAS
AF:
0.800
Gnomad SAS
AF:
0.718
Gnomad FIN
AF:
0.810
Gnomad MID
AF:
0.642
Gnomad NFE
AF:
0.719
Gnomad OTH
AF:
0.657
GnomAD4 exome
AF:
0.717
AC:
261519
AN:
364764
Hom.:
94890
Cov.:
4
AF XY:
0.718
AC XY:
137961
AN XY:
192140
show subpopulations
Gnomad4 AFR exome
AF:
0.403
Gnomad4 AMR exome
AF:
0.773
Gnomad4 ASJ exome
AF:
0.678
Gnomad4 EAS exome
AF:
0.789
Gnomad4 SAS exome
AF:
0.699
Gnomad4 FIN exome
AF:
0.801
Gnomad4 NFE exome
AF:
0.718
Gnomad4 OTH exome
AF:
0.696
GnomAD4 genome
AF:
0.646
AC:
98176
AN:
151910
Hom.:
33343
Cov.:
31
AF XY:
0.654
AC XY:
48523
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.412
Gnomad4 AMR
AF:
0.754
Gnomad4 ASJ
AF:
0.679
Gnomad4 EAS
AF:
0.800
Gnomad4 SAS
AF:
0.718
Gnomad4 FIN
AF:
0.810
Gnomad4 NFE
AF:
0.719
Gnomad4 OTH
AF:
0.661
Alfa
AF:
0.682
Hom.:
12011
Bravo
AF:
0.628
Asia WGS
AF:
0.752
AC:
2604
AN:
3462

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Deficiency of butyrylcholinesterase Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.6
DANN
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3495; hg19: chr3-165490981; API