Variant X-24575238-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_004845.5(PCYT1B):c.789T>C(p.Phe263=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000945 in 1,206,214 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 33 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., 5 hem., cov: 23)

Exomes 𝑓: 0.000088 ( 0 hom. 28 hem. )

Consequence

PCYT1B
NM_004845.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.18

Variant links:

Genes affected

PCYT1B (HGNC:8755): (phosphate cytidylyltransferase 1B, choline) The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

PCYT1B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant X-24575238-A-G is Benign according to our data. Variant chrX-24575238-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2660194.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PCYT1B	NM_004845.5 linkuse as main transcript	c.789T>C	p.Phe263=	synonymous_variant	7/8	ENST00000379144.7
PCYT1B	NM_001163264.2 linkuse as main transcript	c.735T>C	p.Phe245=	synonymous_variant	7/8
PCYT1B	NM_001163265.2 linkuse as main transcript	c.789T>C	p.Phe263=	synonymous_variant	7/9
PCYT1B	XM_017029977.2 linkuse as main transcript	c.501T>C	p.Phe167=	synonymous_variant	8/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCYT1B	ENST00000379144.7 linkuse as main transcript	c.789T>C	p.Phe263=	synonymous_variant	7/8	1	NM_004845.5	P1	Q9Y5K3-1
PCYT1B	ENST00000379145.5 linkuse as main transcript	c.735T>C	p.Phe245=	synonymous_variant	7/8	1			Q9Y5K3-4
PCYT1B	ENST00000356768.8 linkuse as main transcript	c.789T>C	p.Phe263=	synonymous_variant	7/9	1			Q9Y5K3-2
PCYT1B	ENST00000496020.1 linkuse as main transcript	c.*98T>C		3_prime_UTR_variant, NMD_transcript_variant	6/7	3

Frequencies

GnomAD3 genomes

AF:

0.000161

AC:

AN:

111790

Hom.:

Cov.:

AF XY:

0.000147

AC XY:

AN XY:

33962

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00292

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000301

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000887

AC:

AN:

180466

Hom.:

AF XY:

0.0000769

AC XY:

AN XY:

65052

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000553

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000185

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000877

AC:

AN:

1094424

Hom.:

Cov.:

AF XY:

0.0000778

AC XY:

AN XY:

359874

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000186

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000110

Gnomad4 OTH exome

AF:

0.0000653

GnomAD4 genome

AF:

0.000161

AC:

AN:

111790

Hom.:

Cov.:

AF XY:

0.000147

AC XY:

AN XY:

33962

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000301

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000217

Hom.:

Bravo

AF:

0.000128

EpiCase

AF:

0.000719

EpiControl

AF:

0.000420

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

PCYT1B: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

Cadd

Benign

Dann

Benign

0.76

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