chrX-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
NM_004845.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.453
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
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
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
?
Synonymous conserved (PhyloP=-0.453 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.1041C>T | p.Pro347= | synonymous_variant | 8/8 | ENST00000379144.7 | |
PCYT1B | NM_001163264.2 | c.987C>T | p.Pro329= | synonymous_variant | 8/8 | ||
PCYT1B | XM_017029977.2 | c.753C>T | p.Pro251= | synonymous_variant | 9/9 | ||
PCYT1B | NM_001163265.2 | c.960+81C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.1041C>T | p.Pro347= | synonymous_variant | 8/8 | 1 | NM_004845.5 | P1 | |
PCYT1B | ENST00000379145.5 | c.987C>T | p.Pro329= | synonymous_variant | 8/8 | 1 | |||
PCYT1B | ENST00000356768.8 | c.960+81C>T | intron_variant | 1 | |||||
PCYT1B | ENST00000496020.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000555 AC: 62AN: 111732Hom.: 0 Cov.: 23 AF XY: 0.000472 AC XY: 16AN XY: 33902
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GnomAD3 exomes AF: 0.000562 AC: 82AN: 145962Hom.: 0 AF XY: 0.000399 AC XY: 17AN XY: 42652
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GnomAD4 exome AF: 0.000871 AC: 927AN: 1064214Hom.: 1 Cov.: 30 AF XY: 0.000825 AC XY: 283AN XY: 342836
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GnomAD4 genome ? AF: 0.000555 AC: 62AN: 111785Hom.: 0 Cov.: 23 AF XY: 0.000471 AC XY: 16AN XY: 33965
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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, BP7, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at