chrX-24590181-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004845.5(PCYT1B):c.335-7G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000916 in 1,091,892 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004845.5 splice_region, splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.335-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379144.7 | |||
PCYT1B | NM_001163264.2 | c.281-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PCYT1B | NM_001163265.2 | c.335-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PCYT1B | XM_017029977.2 | c.47-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.335-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004845.5 | P1 | |||
PCYT1B | ENST00000356768.8 | c.335-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
PCYT1B | ENST00000379145.5 | c.281-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
PCYT1B | ENST00000496020.1 | c.257-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 177782Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62622
GnomAD4 exome AF: 0.00000916 AC: 10AN: 1091892Hom.: 0 Cov.: 28 AF XY: 0.0000112 AC XY: 4AN XY: 357500
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | PCYT1B: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at