chr5-68293098-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_181523.3(PIK3R1):c.1020-3C>T 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 0.000278 in 1,606,906 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_181523.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R1 | NM_181523.3 | c.1020-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000521381.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R1 | ENST00000521381.6 | c.1020-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_181523.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000303 AC: 46AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 76AN: 251024Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135688
GnomAD4 exome AF: 0.000276 AC: 401AN: 1454906Hom.: 0 Cov.: 29 AF XY: 0.000272 AC XY: 197AN XY: 724236
GnomAD4 genome AF: 0.000303 AC: 46AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.000216 AC XY: 16AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 02, 2017 | - - |
SHORT syndrome;C3554689:Agammaglobulinemia 7, autosomal recessive;C4014934:Immunodeficiency 36 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at