rs28691121
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000342991.10(ENSG00000290788):n.1081+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 1,501,740 control chromosomes in the GnomAD database, including 7,988 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.099 ( 1188 hom., cov: 29)
Exomes 𝑓: 0.063 ( 6800 hom. )
Consequence
ENSG00000290788
ENST00000342991.10 intron
ENST00000342991.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.62
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP21A1P | NR_040090.1 | n.1081+30G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000290788 | ENST00000342991.10 | n.1081+30G>A | intron_variant | 3 | ||||||
CYP21A1P | ENST00000354927.4 | n.643+30G>A | intron_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0989 AC: 14185AN: 143426Hom.: 1183 Cov.: 29
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GnomAD3 exomes AF: 0.0653 AC: 10527AN: 161144Hom.: 875 AF XY: 0.0637 AC XY: 5458AN XY: 85702
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GnomAD4 exome AF: 0.0628 AC: 85308AN: 1358200Hom.: 6800 Cov.: 35 AF XY: 0.0623 AC XY: 41814AN XY: 670754
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GnomAD4 genome AF: 0.0991 AC: 14224AN: 143540Hom.: 1188 Cov.: 29 AF XY: 0.0999 AC XY: 6991AN XY: 69960
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at