rs706714
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_181523.3(PIK3R1):c.334+14A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,578,110 control chromosomes in the GnomAD database, including 69,982 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_181523.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PIK3R1 | NM_181523.3 | c.334+14A>C | intron_variant | Intron 2 of 15 | ENST00000521381.6 | NP_852664.1 | ||
PIK3R1 | XM_005248542.4 | c.334+14A>C | intron_variant | Intron 2 of 15 | XP_005248599.1 | |||
PIK3R1 | XM_017009585.3 | c.334+14A>C | intron_variant | Intron 2 of 15 | XP_016865074.1 | |||
PIK3R1 | XM_047417315.1 | c.334+14A>C | intron_variant | Intron 2 of 15 | XP_047273271.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.316 AC: 48083AN: 151966Hom.: 8259 Cov.: 32
GnomAD3 exomes AF: 0.324 AC: 72805AN: 224782Hom.: 13619 AF XY: 0.317 AC XY: 38786AN XY: 122348
GnomAD4 exome AF: 0.280 AC: 399831AN: 1426026Hom.: 61693 Cov.: 29 AF XY: 0.281 AC XY: 198498AN XY: 707548
GnomAD4 genome AF: 0.317 AC: 48151AN: 152084Hom.: 8289 Cov.: 32 AF XY: 0.321 AC XY: 23858AN XY: 74352
ClinVar
Submissions by phenotype
not specified Benign:3
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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This variant is classified as Benign based on local population frequency. This variant was detected in 54% of patients studied by a panel of primary immunodeficiencies. Number of patients: 52. Only high quality variants are reported. -
not provided Benign:2
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Agammaglobulinemia 7, autosomal recessive Benign:1
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SHORT syndrome Benign:1
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SHORT syndrome;C3554689:Agammaglobulinemia 7, autosomal recessive;C4014934:Immunodeficiency 36 Benign:1
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Immunodeficiency 36 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at