Genetic Variant CEPT1:p.Ile120Val (chr1-111159398-A-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_006090.5(CEPT1):c.358A>G(p.Ile120Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00985 in 1,612,082 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 5 hom., cov: 31)

Exomes 𝑓: 0.010 ( 96 hom. )

Consequence

CEPT1
NM_006090.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.733

Variant links:

Genes affected

CEPT1 (HGNC:24289): (choline/ethanolamine phosphotransferase 1) This gene codes for a choline/ethanolaminephosphotransferase, which functions in the synthesis of choline- or ethanolamine- containing phospholipids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

CEPT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0056552887).

BP6

Variant 1-111159398-A-G is Benign according to our data. Variant chr1-111159398-A-G is described in ClinVar as [Benign]. Clinvar id is 775055.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEPT1	NM_006090.5 link	c.358A>G	p.Ile120Val	missense_variant	Exon 3 of 9	ENST00000357172.9	NP_006081.1	Q9Y6K0A1PL14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEPT1	ENST00000357172.9 link	c.358A>G	p.Ile120Val	missense_variant	Exon 3 of 9	1	NM_006090.5	ENSP00000349696.4		Q9Y6K0

Frequencies

GnomAD3 genomes

AF:

0.00809

AC:

1231

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00224

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0131

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00731

AC:

1821

AN:

249064

Hom.:

AF XY:

0.00755

AC XY:

1017

AN XY:

134754

show subpopulations

Gnomad AFR exome

AF:

0.00161

Gnomad AMR exome

AF:

0.00213

Gnomad ASJ exome

AF:

0.00785

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00113

Gnomad FIN exome

AF:

0.0113

Gnomad NFE exome

AF:

0.0116

Gnomad OTH exome

AF:

0.00796

GnomAD4 exome

AF:

0.0100

AC:

14646

AN:

1459822

Hom.:

Cov.:

AF XY:

0.00987

AC XY:

7170

AN XY:

726254

show subpopulations

Gnomad4 AFR exome

AF:

0.00138

Gnomad4 AMR exome

AF:

0.00262

Gnomad4 ASJ exome

AF:

0.00735

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000955

Gnomad4 FIN exome

AF:

0.0117

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.00910

GnomAD4 genome

AF:

0.00808

AC:

1231

AN:

152260

Hom.:

Cov.:

AF XY:

0.00760

AC XY:

566

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00224

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00922

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.0136

Gnomad4 NFE

AF:

0.0131

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.0110

Hom.:

Bravo

AF:

0.00669

TwinsUK

AF:

0.0113

AC:

ALSPAC

AF:

0.0117

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.0126

AC:

108

ExAC

AF:

0.00750

AC:

911

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.0101

EpiControl

AF:

0.0108

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 02, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.087

T;T;T

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.42

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.72

T;.;T

MetaRNN

Benign

0.0057

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.060

N;N;.

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.69

N;N;.

REVEL

Benign

0.092

Sift

Benign

0.13

T;T;.

Sift4G

Benign

0.36

T;T;T

Polyphen

0.0030

B;B;.

Vest4

0.17

MVP

0.12

MPC

0.16

ClinPred

0.0032

GERP RS

-0.064

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.029

gMVP

0.13

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over