Variant chr12-101723803-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020244.3(CHPT1):c.1021T>C(p.Phe341Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00266 in 1,544,868 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 70 hom. )

Consequence

CHPT1
NM_020244.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 5.93

Variant links:

Genes affected

CHPT1 (HGNC:17852): (choline phosphotransferase 1) Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

CHPT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008994997).

BP6

Variant 12-101723803-T-C is Benign according to our data. Variant chr12-101723803-T-C is described in ClinVar as [Benign]. Clinvar id is 782716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHPT1	NM_020244.3 linkuse as main transcript	c.1021T>C	p.Phe341Leu	missense_variant	7/9	ENST00000229266.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHPT1	ENST00000229266.8 linkuse as main transcript	c.1021T>C	p.Phe341Leu	missense_variant	7/9	1	NM_020244.3	P1	Q8WUD6-1

Frequencies

GnomAD3 genomes

AF:

0.00319

AC:

486

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00229

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0529

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00847

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000779

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00655

AC:

1597

AN:

243758

Hom.:

AF XY:

0.00619

AC XY:

815

AN XY:

131722

show subpopulations

Gnomad AFR exome

AF:

0.000190

Gnomad AMR exome

AF:

0.00459

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0595

Gnomad SAS exome

AF:

0.00196

Gnomad FIN exome

AF:

0.00908

Gnomad NFE exome

AF:

0.00121

Gnomad OTH exome

AF:

0.00319

GnomAD4 exome

AF:

0.00260

AC:

3626

AN:

1392530

Hom.:

Cov.:

AF XY:

0.00252

AC XY:

1758

AN XY:

696608

show subpopulations

Gnomad4 AFR exome

AF:

0.000129

Gnomad4 AMR exome

AF:

0.00478

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0553

Gnomad4 SAS exome

AF:

0.00227

Gnomad4 FIN exome

AF:

0.00839

Gnomad4 NFE exome

AF:

0.000409

Gnomad4 OTH exome

AF:

0.00329

GnomAD4 genome

AF:

0.00318

AC:

484

AN:

152338

Hom.:

Cov.:

AF XY:

0.00372

AC XY:

277

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.00229

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0528

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.00847

Gnomad4 NFE

AF:

0.000779

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00319

Hom.:

Bravo

AF:

0.00345

ExAC

AF:

0.00633

AC:

768

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.000274

EpiControl

AF:

0.000239

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 22, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.92

BayesDel_addAF

Benign

-0.17

BayesDel_noAF

Uncertain

0.020

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.13

T;.

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.55

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

D;.

MetaRNN

Benign

0.0090

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.4

M;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.67

PROVEAN

Pathogenic

-5.5

D;D

REVEL

Uncertain

0.45

Sift

Benign

0.047

D;D

Sift4G

Benign

0.066

T;T

Polyphen

1.0

D;D

Vest4

0.44

MutPred

0.53

Gain of catalytic residue at F336 (P = 0.0077);Gain of catalytic residue at F336 (P = 0.0077);

MVP

0.74

MPC

0.38

ClinPred

0.085

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.52

gMVP

0.60

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