16-66935658-CG-GT

Variant names:

• chr16-66935658-CG-GT
• NM_001365405.1:c.23_24delCGinsGT
• CES2 p.Ala8Gly

Variant summary

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

The NM_001365405.1(CES2):​c.23_24delCGinsGT​(p.Ala8Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A8E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CES2 NM_001365405.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 0 publications found

Genes affected

CES2 (HGNC:1864): (carboxylesterase 2) This gene encodes a member of the carboxylesterase large family. The family members are responsible for the hydrolysis or transesterification of various xenobiotics, such as cocaine and heroin, and endogenous substrates with ester, thioester, or amide bonds. They may participate in fatty acyl and cholesterol ester metabolism, and may play a role in the blood-brain barrier system. The protein encoded by this gene is the major intestinal enzyme and functions in intestine drug clearance. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365405.1. 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
	CES2	NM_001365405.1	MANE Select	c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	NP_001352334.1	O00748-1
	CES2	NM_003869.6		c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	NP_003860.3
	CES2	NM_198061.3		c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	NP_932327.2	O00748-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CES2	ENST00000317091.10	TSL:1 MANE Select	c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	ENSP00000317842.5	O00748-1
	CES2	ENST00000417689.6	TSL:1	c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	ENSP00000394452.2	O00748-2
	CES2	ENST00000971765.1		c.23_24delCGinsGT	p.Ala8Gly	missense	N/A	ENSP00000641824.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-66969561;