chr3-165788069-T-C

Position:

• chr3-165788069-T-C

Variant summary

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

The NM_000055.4(BCHE):​c.1518-1758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,782 control chromosomes in the GnomAD database, including 34,707 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 0.65 (34707 hom., cov: 31)
• Consequence: BCHE NM_000055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCHE	NM_000055.4	c.1518-1758A>G		intron_variant		ENST00000264381.8	NP_000046.1
BCHE	NR_137635.2	n.111-1758A>G		intron_variant, non_coding_transcript_variant
BCHE	NR_137636.2	n.1636-1758A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCHE	ENST00000264381.8	c.1518-1758A>G		intron_variant		1	NM_000055.4	ENSP00000264381	P1
LINC01322	ENST00000651449.1	n.1008-57823T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.653 AC: 98978 AN: 151664 Hom.: 34687 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.652 AC: 99016 AN: 151782 Hom.: 34707 Cov.: 31 AF XY: 0.660 AC XY: 48954 AN XY: 74190

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.665

Alfa AF: 0.695 Hom.: 4731

Bravo AF: 0.627

Asia WGS AF: 0.712 AC: 2471 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.66

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: rs1355534; hg19: chr3-165505857;