3-165782897-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCHE	NM_000055.4	c.1684+3248G>A		intron_variant	Intron 3 of 3	ENST00000264381.8	NP_000046.1
BCHE	NR_137635.2	n.277+3248G>A		intron_variant	Intron 2 of 2
BCHE	NR_137636.2	n.1802+3248G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCHE	ENST00000264381.8	c.1684+3248G>A		intron_variant	Intron 3 of 3	1	NM_000055.4	ENSP00000264381.3

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

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.000776

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.0641

Alfa AF: 0.0533 Hom.: 205

Bravo AF: 0.0606

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.70

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: rs3863086; hg19: chr3-165500685;