3-172667903-C-T

Position:

• chr3-172667903-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCEH1	NM_020792.6	c.139-19789G>A		intron_variant		ENST00000475381.7
LOC124909457	XR_007096170.1	n.224+1221C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCEH1	ENST00000475381.7	c.139-19789G>A		intron_variant		1	NM_020792.6	P1

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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.200

Alfa AF: 0.246 Hom.: 4422

Bravo AF: 0.189

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.5
DANN	Benign	0.87

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: rs11712263; hg19: chr3-172385693;