X-24647045-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004845.5(PCYT1B):c.61G>A(p.Glu21Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000207 in 1,209,119 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.61G>A | p.Glu21Lys | missense_variant | Exon 1 of 8 | ENST00000379144.7 | NP_004836.2 | |
PCYT1B | NM_001163265.2 | c.61G>A | p.Glu21Lys | missense_variant | Exon 1 of 9 | NP_001156737.1 | ||
PCYT1B | XM_017029977.2 | c.-348G>A | 5_prime_UTR_variant | Exon 1 of 9 | XP_016885466.1 | |||
PCYT1B | NM_001163264.2 | c.63+25525G>A | intron_variant | Intron 1 of 7 | NP_001156736.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.61G>A | p.Glu21Lys | missense_variant | Exon 1 of 8 | 1 | NM_004845.5 | ENSP00000368439.2 | ||
PCYT1B | ENST00000356768.8 | c.61G>A | p.Glu21Lys | missense_variant | Exon 1 of 9 | 1 | ENSP00000349211.4 | |||
PCYT1B | ENST00000379145.5 | c.63+25525G>A | intron_variant | Intron 1 of 7 | 1 | ENSP00000368440.1 | ||||
PCYT1B | ENST00000496020.1 | n.-18G>A | upstream_gene_variant | 3 | ENSP00000436562.1 |
Frequencies
GnomAD3 genomes AF: 0.000116 AC: 13AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33993
GnomAD3 exomes AF: 0.0000655 AC: 12AN: 183318Hom.: 0 AF XY: 0.0000886 AC XY: 6AN XY: 67754
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097320Hom.: 0 Cov.: 29 AF XY: 0.00000827 AC XY: 3AN XY: 362686
GnomAD4 genome AF: 0.000116 AC: 13AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33993
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.61G>A (p.E21K) alteration is located in exon 1 (coding exon 1) of the PCYT1B gene. This alteration results from a G to A substitution at nucleotide position 61, causing the glutamic acid (E) at amino acid position 21 to be replaced by a lysine (K). 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