3-165804028-G-C

Position:

• chr3-165804028-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000055.4(BCHE):​c.1518-17717C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 147,636 control chromosomes in the GnomAD database, including 764 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 0.099 (764 hom., cov: 31)
• Consequence: BCHE NM_000055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCHE	NM_000055.4	c.1518-17717C>G		intron_variant		ENST00000264381.8	NP_000046.1
BCHE	NR_137635.2	n.111-17717C>G		intron_variant, non_coding_transcript_variant
BCHE	NR_137636.2	n.1636-17717C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCHE	ENST00000264381.8	c.1518-17717C>G		intron_variant		1	NM_000055.4	ENSP00000264381	P1
LINC01322	ENST00000651449.1	n.1008-41864G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14549 AN: 147520 Hom.: 760 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0299

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0986 AC: 14561 AN: 147636 Hom.: 764 Cov.: 31 AF XY: 0.0981 AC XY: 7021 AN XY: 71592

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0878

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0827 Hom.: 66

Bravo AF: 0.106

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.62

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: rs12487357; hg19: chr3-165521816;