chrX-24590024-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004845.5(PCYT1B):c.485A>G(p.Lys162Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000092 in 1,087,370 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004845.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.485A>G | p.Lys162Arg | missense_variant, splice_region_variant | 4/8 | ENST00000379144.7 | |
PCYT1B | NM_001163264.2 | c.431A>G | p.Lys144Arg | missense_variant, splice_region_variant | 4/8 | ||
PCYT1B | NM_001163265.2 | c.485A>G | p.Lys162Arg | missense_variant, splice_region_variant | 4/9 | ||
PCYT1B | XM_017029977.2 | c.197A>G | p.Lys66Arg | missense_variant, splice_region_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.485A>G | p.Lys162Arg | missense_variant, splice_region_variant | 4/8 | 1 | NM_004845.5 | P1 | |
PCYT1B | ENST00000379145.5 | c.431A>G | p.Lys144Arg | missense_variant, splice_region_variant | 4/8 | 1 | |||
PCYT1B | ENST00000356768.8 | c.485A>G | p.Lys162Arg | missense_variant, splice_region_variant | 4/9 | 1 | |||
PCYT1B | ENST00000496020.1 | c.407A>G | p.Lys136Arg | missense_variant, splice_region_variant, NMD_transcript_variant | 4/7 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 exomes AF: 0.00000575 AC: 1AN: 173781Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 59105
GnomAD4 exome AF: 9.20e-7 AC: 1AN: 1087370Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 353734
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.485A>G (p.K162R) alteration is located in exon 4 (coding exon 4) of the PCYT1B gene. This alteration results from a A to G substitution at nucleotide position 485, causing the lysine (K) at amino acid position 162 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at