chrX-24619030-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004845.5(PCYT1B):c.172C>A(p.Pro58Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000233 in 1,074,571 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.000023 ( 0 hom. 12 hem. )
Consequence
PCYT1B
NM_004845.5 missense
NM_004845.5 missense
Scores
2
6
7
Clinical Significance
Conservation
PhyloP100: 8.46
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.113711715).
BS2
?
High Hemizygotes in GnomAdExome at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.172C>A | p.Pro58Thr | missense_variant | 2/8 | ENST00000379144.7 | |
PCYT1B | NM_001163264.2 | c.118C>A | p.Pro40Thr | missense_variant | 2/8 | ||
PCYT1B | NM_001163265.2 | c.172C>A | p.Pro58Thr | missense_variant | 2/9 | ||
PCYT1B | XM_017029977.2 | c.-117C>A | 5_prime_UTR_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.172C>A | p.Pro58Thr | missense_variant | 2/8 | 1 | NM_004845.5 | P1 | |
PCYT1B | ENST00000379145.5 | c.118C>A | p.Pro40Thr | missense_variant | 2/8 | 1 | |||
PCYT1B | ENST00000356768.8 | c.172C>A | p.Pro58Thr | missense_variant | 2/9 | 1 | |||
PCYT1B | ENST00000496020.1 | c.94C>A | p.Pro32Thr | missense_variant, NMD_transcript_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD3 exomes AF: 0.0000788 AC: 13AN: 165022Hom.: 0 AF XY: 0.000115 AC XY: 6AN XY: 52346
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GnomAD4 exome AF: 0.0000233 AC: 25AN: 1074571Hom.: 0 Cov.: 26 AF XY: 0.0000348 AC XY: 12AN XY: 345107
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GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ExAC
?
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10
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.172C>A (p.P58T) alteration is located in exon 2 (coding exon 2) of the PCYT1B gene. This alteration results from a C to A substitution at nucleotide position 172, causing the proline (P) at amino acid position 58 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0020, 0.0030
.;B;B
Vest4
MutPred
0.38
.;Gain of helix (P = 0.0143);Gain of helix (P = 0.0143);
MVP
MPC
0.0028
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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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