3-165773088-G-GA

Position:

• chr3-165773088-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000055.4(BCHE):​c.*293_*294insT 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.803

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)

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
BCHE	NM_000055.4	c.*293_*294insT		3_prime_UTR_variant	4/4	ENST00000264381.8
BCHE	NR_137635.2	n.695_696insT		non_coding_transcript_exon_variant	3/3
BCHE	NR_137636.2	n.2299_2300insT		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCHE	ENST00000264381.8	c.*293_*294insT		3_prime_UTR_variant	4/4	1	NM_000055.4	P1
LINC01322	ENST00000651449.1	n.1008-72799dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138646 AN: 151908 Hom.: 63779 Cov.: 0

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.: 3 AF XY: 0.950 AC XY: 41271 AN XY: 43438

Gnomad4 AFR exome AF: 0.779

Gnomad4 AMR exome AF: 0.951

Gnomad4 ASJ exome AF: 0.963

Gnomad4 EAS exome AF: 0.922

Gnomad4 SAS exome AF: 0.913

Gnomad4 FIN exome AF: 0.986

Gnomad4 NFE exome AF: 0.965

Gnomad4 OTH exome AF: 0.946

GnomAD4 genome AF: 0.913 AC: 138737 AN: 152026 Hom.: 63813 Cov.: 0 AF XY: 0.915 AC XY: 67988 AN XY: 74294

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.927

Asia WGS AF: 0.924 AC: 3182 AN: 3444

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Deficiency of butyrylcholinesterase Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3836432; hg19: chr3-165490876;