rs11712263

Variant names:

• chr3-172667903-C-T
• rs11712263
• NM_020792.6:c.139-19789G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020792.6(NCEH1):​c.139-19789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,076 control chromosomes in the GnomAD database, including 3,275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3275 hom., cov: 32)
• Consequence: NCEH1 NM_020792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 7 publications found

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]

LOC124909457 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020792.6. 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
	NCEH1	NM_020792.6	MANE Select	c.139-19789G>A		intron	N/A	NP_065843.4
	NCEH1	NM_001146276.3		c.139-19789G>A		intron	N/A	NP_001139748.2	Q6PIU2-2
	NCEH1	NM_001146277.3		c.-251-19789G>A		intron	N/A	NP_001139749.1	Q6PIU2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCEH1	ENST00000475381.7	TSL:1 MANE Select	c.139-19789G>A		intron	N/A	ENSP00000418571.4	Q6PIU2-1
	NCEH1	ENST00000538775.5	TSL:2	c.235-19789G>A		intron	N/A	ENSP00000442464.1	A0A0A0MTJ9
	NCEH1	ENST00000894447.1		c.139-19789G>A		intron	N/A	ENSP00000564506.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29931 AN: 151958 Hom.: 3278 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.197 AC: 29935 AN: 152076 Hom.: 3275 Cov.: 32 AF XY: 0.194 AC XY: 14435 AN XY: 74308

African (AFR) AF: 0.106 AC: 4382 AN: 41500

American (AMR) AF: 0.163 AC: 2496 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3464

East Asian (EAS) AF: 0.126 AC: 655 AN: 5178

South Asian (SAS) AF: 0.236 AC: 1133 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2341 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17418 AN: 67964

Other (OTH) AF: 0.200 AC: 423 AN: 2114

Alfa AF: 0.223 Hom.: 6664

Bravo AF: 0.189

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.5
DANN	Benign	0.87
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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: rs11712263; hg19: chr3-172385693;