3-165826514-G-C

Variant names:

• chr3-165826514-G-C
• rs2048493
• NM_000055.4:c.1517+3003C>G

Variant summary

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

The NM_000055.4(BCHE):​c.1517+3003C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,602 control chromosomes in the GnomAD database, including 24,595 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 0.55 (24595 hom., cov: 30)
• Consequence: BCHE NM_000055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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.1517+3003C>G		intron	N/A	NP_000046.1	P06276
	BCHE	NR_137635.2		n.110+10800C>G		intron	N/A
	BCHE	NR_137636.2		n.1635+3003C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCHE	ENST00000264381.8	TSL:1 MANE Select	c.1517+3003C>G		intron	N/A	ENSP00000264381.3	P06276
	BCHE	ENST00000479451.5	TSL:1	c.107+10800C>G		intron	N/A	ENSP00000418325.1	H0Y885
	BCHE	ENST00000855337.1		c.1517+3003C>G		intron	N/A	ENSP00000525396.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82610 AN: 151484 Hom.: 24574 Cov.: 30

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.545 AC: 82653 AN: 151602 Hom.: 24595 Cov.: 30 AF XY: 0.551 AC XY: 40809 AN XY: 74052

African (AFR) AF: 0.280 AC: 11550 AN: 41318

American (AMR) AF: 0.609 AC: 9252 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2104 AN: 3440

East Asian (EAS) AF: 0.666 AC: 3430 AN: 5150

South Asian (SAS) AF: 0.638 AC: 3061 AN: 4798

European-Finnish (FIN) AF: 0.729 AC: 7687 AN: 10542

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43592 AN: 67868

Other (OTH) AF: 0.544 AC: 1140 AN: 2096

Alfa AF: 0.474 Hom.: 1506

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.39
PhyloP100		-0.58
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: rs2048493; hg19: chr3-165544302;