3-172633600-C-T

Variant names:

• chr3-172633600-C-T
• NM_020792.6:c.1102G>A

Variant summary

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

The NM_020792.6(NCEH1):​c.1102G>A​(p.Val368Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NCEH1 NM_020792.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.57

Genes affected

NCEH1 (HGNC:29260): (neutral cholesterol ester hydrolase 1) Predicted to enable hydrolase activity. Predicted to be involved in ether lipid metabolic process. Predicted to act upstream of or within SMAD protein signal transduction; protein dephosphorylation; and xenobiotic metabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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
NCEH1	NM_020792.6	c.1102G>A	p.Val368Met	missense_variant	Exon 5 of 5	ENST00000475381.7	NP_065843.4
NCEH1	NM_001146276.3	c.1126G>A	p.Val376Met	missense_variant	Exon 5 of 5		NP_001139748.2
NCEH1	NM_001146277.3	c.703G>A	p.Val235Met	missense_variant	Exon 5 of 5		NP_001139749.1
NCEH1	NM_001146278.3	c.703G>A	p.Val235Met	missense_variant	Exon 4 of 4		NP_001139750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCEH1	ENST00000475381.7	c.1102G>A	p.Val368Met	missense_variant	Exon 5 of 5	1	NM_020792.6	ENSP00000418571.4
NCEH1	ENST00000538775.5	c.1222G>A	p.Val408Met	missense_variant	Exon 5 of 5	2		ENSP00000442464.1
NCEH1	ENST00000543711.5	c.703G>A	p.Val235Met	missense_variant	Exon 4 of 4	2		ENSP00000443227.1
NCEH1	ENST00000470419.1	n.*175G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Aug 15, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1222G>A (p.V408M) alteration is located in exon 5 (coding exon 5) of the NCEH1 gene. This alteration results from a G to A substitution at nucleotide position 1222, causing the valine (V) at amino acid position 408 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.57
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Uncertain	0.12
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.36	T;.;.
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.44	T;T;T
MetaSVM	Benign	-0.58	T
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-2.9	.;D;D
REVEL	Uncertain	0.54
Sift	Uncertain	0.0010	.;D;D
Sift4G	Uncertain	0.0020	D;D;D
Vest4		0.70
MVP		0.75
MPC		1.1
ClinPred		0.98	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-172351390; COSMIC: COSV56434422; COSMIC: COSV56434422;