rs886058154

Variant names:

• chr3-165773208-G-A
• rs886058154
• NM_000055.4:c.*174C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-165773208-G-A
• chr3-165773208-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000055.4(BCHE):​c.*174C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000239 in 419,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: BCHE NM_000055.4 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.62
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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.*174C>T		3_prime_UTR	Exon 4 of 4	NP_000046.1	P06276
	BCHE	NR_137635.2		n.576C>T		non_coding_transcript_exon	Exon 3 of 3
	BCHE	NR_137636.2		n.2180C>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCHE	ENST00000264381.8	TSL:1 MANE Select	c.*174C>T		3_prime_UTR	Exon 4 of 4	ENSP00000264381.3	P06276
	BCHE	ENST00000479451.5	TSL:1	c.*174C>T		3_prime_UTR	Exon 3 of 3	ENSP00000418325.1	H0Y885
	BCHE	ENST00000855337.1		c.*174C>T		3_prime_UTR	Exon 5 of 5	ENSP00000525396.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000239 AC: 1 AN: 419268 Hom.: 0 Cov.: 5 AF XY: 0.00000453 AC XY: 1 AN XY: 220800

African (AFR) AF: 0.00 AC: 0 AN: 11436

American (AMR) AF: 0.00 AC: 0 AN: 14282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12404

East Asian (EAS) AF: 0.00 AC: 0 AN: 28100

South Asian (SAS) AF: 0.0000281 AC: 1 AN: 35648

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27806

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1818

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 263860

Other (OTH) AF: 0.00 AC: 0 AN: 23914

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Deficiency of butyrylcholinesterase (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.41
PhyloP100		1.6

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: rs886058154; hg19: chr3-165490996;