X-48898097-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001032383.2(PQBP1):c.-19+4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0581 in 1,021,160 control chromosomes in the GnomAD database, including 1,362 homozygotes. There are 17,562 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 Benign (★★).
Frequency
Consequence
NM_001032383.2 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PQBP1 | NM_001032382.2 | c.-19+15G>A | intron_variant | Intron 1 of 6 | ENST00000447146.7 | NP_001027554.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0432 AC: 4780AN: 110734Hom.: 110 Cov.: 23 AF XY: 0.0397 AC XY: 1307AN XY: 32940
GnomAD4 exome AF: 0.0599 AC: 54576AN: 910372Hom.: 1252 Cov.: 29 AF XY: 0.0589 AC XY: 16253AN XY: 275964
GnomAD4 genome AF: 0.0431 AC: 4779AN: 110788Hom.: 110 Cov.: 23 AF XY: 0.0397 AC XY: 1309AN XY: 33004
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at