chrX-24619040-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004845.5(PCYT1B):c.162G>C(p.Gln54His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,190,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004845.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.162G>C | p.Gln54His | missense_variant | 2/8 | ENST00000379144.7 | |
PCYT1B | NM_001163264.2 | c.108G>C | p.Gln36His | missense_variant | 2/8 | ||
PCYT1B | NM_001163265.2 | c.162G>C | p.Gln54His | missense_variant | 2/9 | ||
PCYT1B | XM_017029977.2 | c.-127G>C | 5_prime_UTR_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.162G>C | p.Gln54His | missense_variant | 2/8 | 1 | NM_004845.5 | P1 | |
PCYT1B | ENST00000379145.5 | c.108G>C | p.Gln36His | missense_variant | 2/8 | 1 | |||
PCYT1B | ENST00000356768.8 | c.162G>C | p.Gln54His | missense_variant | 2/9 | 1 | |||
PCYT1B | ENST00000496020.1 | c.84G>C | p.Gln28His | missense_variant, NMD_transcript_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000448 AC: 5AN: 111693Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33871
GnomAD3 exomes AF: 0.0000238 AC: 4AN: 167796Hom.: 0 AF XY: 0.0000185 AC XY: 1AN XY: 54132
GnomAD4 exome AF: 0.00000927 AC: 10AN: 1078338Hom.: 0 Cov.: 26 AF XY: 0.0000144 AC XY: 5AN XY: 347404
GnomAD4 genome ? AF: 0.0000448 AC: 5AN: 111693Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33871
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.162G>C (p.Q54H) alteration is located in exon 2 (coding exon 2) of the PCYT1B gene. This alteration results from a G to C substitution at nucleotide position 162, causing the glutamine (Q) at amino acid position 54 to be replaced by a histidine (H). 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