rs706713
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_181523.3(PIK3R1):c.219C>T(p.Tyr73Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,613,626 control chromosomes in the GnomAD database, including 66,189 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PIK3R1 | NM_181523.3 | c.219C>T | p.Tyr73Tyr | synonymous_variant | Exon 2 of 16 | ENST00000521381.6 | NP_852664.1 | |
PIK3R1 | XM_005248542.4 | c.219C>T | p.Tyr73Tyr | synonymous_variant | Exon 2 of 16 | XP_005248599.1 | ||
PIK3R1 | XM_017009585.3 | c.219C>T | p.Tyr73Tyr | synonymous_variant | Exon 2 of 16 | XP_016865074.1 | ||
PIK3R1 | XM_047417315.1 | c.219C>T | p.Tyr73Tyr | synonymous_variant | Exon 2 of 16 | XP_047273271.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.314 AC: 47620AN: 151712Hom.: 8301 Cov.: 31
GnomAD3 exomes AF: 0.315 AC: 78832AN: 250638Hom.: 14537 AF XY: 0.305 AC XY: 41414AN XY: 135752
GnomAD4 exome AF: 0.267 AC: 389926AN: 1461796Hom.: 57859 Cov.: 35 AF XY: 0.266 AC XY: 193195AN XY: 727212
GnomAD4 genome AF: 0.314 AC: 47699AN: 151830Hom.: 8330 Cov.: 31 AF XY: 0.318 AC XY: 23571AN XY: 74178
ClinVar
Submissions by phenotype
not provided Benign:3Other:1
This variant is associated with the following publications: (PMID: 17016694) -
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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not specified Benign:3
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. -
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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 -
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