3-165773088-GA-GAAA

Variant names:

• chr3-165773088-G-GAA
• rs3836432
• NM_000055.4:c.*292_*293dupTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000055.4(BCHE):​c.*292_*293dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000036 (0 hom.)
• Consequence: BCHE NM_000055.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 3 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: Uncertain_significance. The variant received 0 ACMG points.

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.*292_*293dupTT		3_prime_UTR	Exon 4 of 4	NP_000046.1	P06276
	BCHE	NR_137635.2		n.694_695dupTT		non_coding_transcript_exon	Exon 3 of 3
	BCHE	NR_137636.2		n.2298_2299dupTT		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.*292_*293dupTT		3_prime_UTR	Exon 4 of 4	ENSP00000264381.3	P06276
	BCHE	ENST00000479451.5	TSL:1	c.*292_*293dupTT		3_prime_UTR	Exon 3 of 3	ENSP00000418325.1	H0Y885
	BCHE	ENST00000855337.1		c.*292_*293dupTT		3_prime_UTR	Exon 5 of 5	ENSP00000525396.1

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 151930 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000360 AC: 3 AN: 83336 Hom.: 0 Cov.: 3 AF XY: 0.0000230 AC XY: 1 AN XY: 43488

African (AFR) AF: 0.00 AC: 0 AN: 2136

American (AMR) AF: 0.00 AC: 0 AN: 3680

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2522

East Asian (EAS) AF: 0.00 AC: 0 AN: 4592

South Asian (SAS) AF: 0.000377 AC: 3 AN: 7956

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4126

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52776

Other (OTH) AF: 0.00 AC: 0 AN: 5236

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 151930 Hom.: 0 Cov.: 0 AF XY: 0.0000270 AC XY: 2 AN XY: 74178

African (AFR) AF: 0.00 AC: 0 AN: 41330

American (AMR) AF: 0.00 AC: 0 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67988

Other (OTH) AF: 0.00 AC: 0 AN: 2086

Alfa AF: 0.00 Hom.: 2125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3836432; hg19: chr3-165490876;