Genetic Variant BCHE:c.*293dupT (chr3-165773088-G-GA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000055.4(BCHE):c.*293dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.91 ( 63813 hom., cov: 0)

Exomes 𝑓: 0.95 ( 37788 hom. )

Consequence

BCHE
NM_000055.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.803

Publications

3 publications found

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]

BCHE links:

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

LINC01322 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 3-165773088-G-GA is Benign according to our data. Variant chr3-165773088-G-GA is described in ClinVar as [Benign]. Clinvar id is 344079.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BCHE	NM_000055.4 link	c.*293dupT	3_prime_UTR_variant	Exon 4 of 4	ENST00000264381.8	NP_000046.1	P06276
BCHE	NR_137635.2 link	n.695dupT	non_coding_transcript_exon_variant	Exon 3 of 3
BCHE	NR_137636.2 link	n.2299dupT	non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCHE	ENST00000264381.8 link	c.*293dupT		3_prime_UTR_variant	Exon 4 of 4	1	NM_000055.4	ENSP00000264381.3		P06276

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138646

AN:

151908

Hom.:

63779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.989

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.969

Gnomad EAS

AF:

0.918

Gnomad SAS

AF:

0.915

Gnomad FIN

AF:

0.986

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.965

Gnomad OTH

AF:

0.927

GnomAD4 exome

AF:

0.952

AC:

79224

AN:

83250

Hom.:

37788

Cov.:

AF XY:

0.950

AC XY:

41271

AN XY:

43438

show subpopulations

African (AFR)

AF:

0.779

AC:

1657

AN:

2128

American (AMR)

AF:

0.951

AC:

3496

AN:

3678

Ashkenazi Jewish (ASJ)

AF:

0.963

AC:

2429

AN:

2522

East Asian (EAS)

AF:

0.922

AC:

4221

AN:

4576

South Asian (SAS)

AF:

0.913

AC:

7256

AN:

7944

European-Finnish (FIN)

AF:

0.986

AC:

4065

AN:

4124

Middle Eastern (MID)

AF:

0.917

AC:

286

AN:

312

European-Non Finnish (NFE)

AF:

0.965

AC:

50864

AN:

52736

Other (OTH)

AF:

0.946

AC:

4950

AN:

5230

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

178

356

533

711

889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.913

AC:

138737

AN:

152026

Hom.:

63813

Cov.:

AF XY:

0.915

AC XY:

67988

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.785

AC:

32511

AN:

41434

American (AMR)

AF:

0.952

AC:

14523

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.969

AC:

3364

AN:

3470

East Asian (EAS)

AF:

0.918

AC:

4742

AN:

5168

South Asian (SAS)

AF:

0.915

AC:

4404

AN:

4812

European-Finnish (FIN)

AF:

0.986

AC:

10447

AN:

10594

Middle Eastern (MID)

AF:

0.912

AC:

268

AN:

294

European-Non Finnish (NFE)

AF:

0.965

AC:

65621

AN:

67978

Other (OTH)

AF:

0.927

AC:

1955

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

555

1111

1666

2222

2777

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.936

Hom.:

2125

Asia WGS

AF:

0.924

AC:

3182

AN:

3444

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Deficiency of butyrylcholinesterase

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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3-165773088-G-GA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over