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GeneBe

X-24562362-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004845.5(PCYT1B):c.1041C>T(p.Pro347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000841 in 1,175,999 control chromosomes in the GnomAD database, including 1 homozygotes. There are 299 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 0.00055 ( 0 hom., 16 hem., cov: 23)
Exomes 𝑓: 0.00087 ( 1 hom. 283 hem. )

Consequence

PCYT1B
NM_004845.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.453
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-24562362-G-A is Benign according to our data. Variant chrX-24562362-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660193.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.453 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 16 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PCYT1BNM_004845.5 linkuse as main transcriptc.1041C>T p.Pro347= synonymous_variant 8/8 ENST00000379144.7
PCYT1BNM_001163264.2 linkuse as main transcriptc.987C>T p.Pro329= synonymous_variant 8/8
PCYT1BXM_017029977.2 linkuse as main transcriptc.753C>T p.Pro251= synonymous_variant 9/9
PCYT1BNM_001163265.2 linkuse as main transcriptc.960+81C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCYT1BENST00000379144.7 linkuse as main transcriptc.1041C>T p.Pro347= synonymous_variant 8/81 NM_004845.5 P1Q9Y5K3-1
PCYT1BENST00000379145.5 linkuse as main transcriptc.987C>T p.Pro329= synonymous_variant 8/81 Q9Y5K3-4
PCYT1BENST00000356768.8 linkuse as main transcriptc.960+81C>T intron_variant 1 Q9Y5K3-2
PCYT1BENST00000496020.1 linkuse as main transcript downstream_gene_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000555
AC:
62
AN:
111732
Hom.:
0
Cov.:
23
AF XY:
0.000472
AC XY:
16
AN XY:
33902
show subpopulations
Gnomad AFR
AF:
0.000130
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000372
Gnomad FIN
AF:
0.000494
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000809
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000562
AC:
82
AN:
145962
Hom.:
0
AF XY:
0.000399
AC XY:
17
AN XY:
42652
show subpopulations
Gnomad AFR exome
AF:
0.000244
Gnomad AMR exome
AF:
0.000447
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000924
Gnomad FIN exome
AF:
0.000531
Gnomad NFE exome
AF:
0.000885
Gnomad OTH exome
AF:
0.000573
GnomAD4 exome
AF:
0.000871
AC:
927
AN:
1064214
Hom.:
1
Cov.:
30
AF XY:
0.000825
AC XY:
283
AN XY:
342836
show subpopulations
Gnomad4 AFR exome
AF:
0.000197
Gnomad4 AMR exome
AF:
0.000554
Gnomad4 ASJ exome
AF:
0.000118
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000627
Gnomad4 FIN exome
AF:
0.000538
Gnomad4 NFE exome
AF:
0.00100
Gnomad4 OTH exome
AF:
0.000964
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000555
AC:
62
AN:
111785
Hom.:
0
Cov.:
23
AF XY:
0.000471
AC XY:
16
AN XY:
33965
show subpopulations
Gnomad4 AFR
AF:
0.000130
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000374
Gnomad4 FIN
AF:
0.000494
Gnomad4 NFE
AF:
0.000810
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000696
Hom.:
5
Bravo
AF:
0.000793

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023PCYT1B: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
Cadd
Benign
6.8
Dann
Benign
0.62

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.

Other links and lift over

dbSNP: rs148789676; hg19: chrX-24580479; API