3-165782897-C-T

Variant names:

• chr3-165782897-C-T
• rs3863086
• NM_000055.4:c.1684+3248G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000055.4(BCHE):​c.1684+3248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 151,874 control chromosomes in the GnomAD database, including 330 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.057 (330 hom., cov: 32)
• Consequence: BCHE NM_000055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000055.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCHE	NM_000055.4	MANE Select	c.1684+3248G>A		intron	N/A	NP_000046.1	P06276
	BCHE	NR_137635.2		n.277+3248G>A		intron	N/A
	BCHE	NR_137636.2		n.1802+3248G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCHE	ENST00000264381.8	TSL:1 MANE Select	c.1684+3248G>A		intron	N/A	ENSP00000264381.3	P06276
	BCHE	ENST00000479451.5	TSL:1	c.274+3248G>A		intron	N/A	ENSP00000418325.1	H0Y885
	BCHE	ENST00000855337.1		c.1747+3248G>A		intron	N/A	ENSP00000525396.1

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8653 AN: 151756 Hom.: 328 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0648

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0570 AC: 8652 AN: 151874 Hom.: 330 Cov.: 32 AF XY: 0.0545 AC XY: 4046 AN XY: 74210

African (AFR) AF: 0.0910 AC: 3772 AN: 41428

American (AMR) AF: 0.0498 AC: 757 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3466

East Asian (EAS) AF: 0.000776 AC: 4 AN: 5152

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4818

European-Finnish (FIN) AF: 0.0113 AC: 119 AN: 10568

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3277 AN: 67922

Other (OTH) AF: 0.0641 AC: 135 AN: 2106

Alfa AF: 0.0551 Hom.: 287

Bravo AF: 0.0606

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.70
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3863086; hg19: chr3-165500685;