rs776903994

Variant names:

• chr16-55810597-T-A
• rs776903994
• NM_001025195.2:c.1238A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-55810597-T-A
• chr16-55810597-T-C
• chr16-55810597-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001025195.2(CES1):​c.1238A>T​(p.Lys413Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CES1 NM_001025195.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

Genes affected

CES1 (HGNC:1863): (carboxylesterase 1) 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. This enzyme is the major liver enzyme and functions in liver drug clearance. Mutations of this gene cause carboxylesterase 1 deficiency. Three transcript variants encoding three different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CES1	NM_001025195.2	c.1238A>T	p.Lys413Ile	missense_variant	Exon 11 of 14	ENST00000360526.8	NP_001020366.1
CES1	NM_001025194.2	c.1235A>T	p.Lys412Ile	missense_variant	Exon 11 of 14		NP_001020365.1
CES1	NM_001266.5	c.1232A>T	p.Lys411Ile	missense_variant	Exon 11 of 14		NP_001257.4
CES1	XM_005255774.3	c.1235A>T	p.Lys412Ile	missense_variant	Exon 11 of 14		XP_005255831.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CES1	ENST00000360526.8	c.1238A>T	p.Lys413Ile	missense_variant	Exon 11 of 14	1	NM_001025195.2	ENSP00000353720.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Benign	-0.027	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.090	.;.;T;T
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.49
FATHMM_MKL	Benign	0.41	N
LIST_S2	Benign	0.77	T;T;T;T
M_CAP	Benign	0.056	D
MetaRNN	Uncertain	0.44	T;T;T;T
MetaSVM	Benign	-0.61	T
MutationAssessor	Benign	1.2	.;.;.;L
PrimateAI	Benign	0.31	T
PROVEAN	Pathogenic	-6.5	D;D;.;D
REVEL	Benign	0.18
Sift	Benign	0.032	D;D;.;D
Sift4G	Benign	0.074	T;T;D;T
Polyphen		0.040	B;.;.;B
Vest4		0.47
MutPred		0.57		.;.;.;Loss of disorder (P = 8e-04);
MVP		0.62
MPC		0.053
ClinPred		0.82	D
GERP RS		1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.65
gMVP		0.29

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: rs776903994; hg19: chr16-55844509;