rs6451
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000500.9(CYP21A2):c.293-67C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,547,130 control chromosomes in the GnomAD database, including 13,939 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1506 hom., cov: 31)
Exomes 𝑓: 0.12 ( 12433 hom. )
Consequence
CYP21A2
NM_000500.9 intron
NM_000500.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.107
Genes affected
CYP21A2 (HGNC:2600): (cytochrome P450 family 21 subfamily A member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and hydroxylates steroids at the 21 position. Its activity is required for the synthesis of steroid hormones including cortisol and aldosterone. Mutations in this gene cause congenital adrenal hyperplasia. A related pseudogene is located near this gene; gene conversion events involving the functional gene and the pseudogene are thought to account for many cases of steroid 21-hydroxylase deficiency. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 6-32039027-C-A is Benign according to our data. Variant chr6-32039027-C-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP21A2 | NM_000500.9 | c.293-67C>A | intron_variant | ENST00000644719.2 | |||
CYP21A2 | NM_001128590.4 | c.203-67C>A | intron_variant | ||||
CYP21A2 | NM_001368143.2 | c.-132-48C>A | intron_variant | ||||
CYP21A2 | NM_001368144.2 | c.-132-48C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP21A2 | ENST00000644719.2 | c.293-67C>A | intron_variant | NM_000500.9 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.131 AC: 19833AN: 151620Hom.: 1507 Cov.: 31
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GnomAD3 exomes AF: 0.125 AC: 20759AN: 166540Hom.: 1938 AF XY: 0.134 AC XY: 11958AN XY: 89052
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GnomAD4 exome AF: 0.117 AC: 162735AN: 1395394Hom.: 12433 Cov.: 40 AF XY: 0.121 AC XY: 83336AN XY: 689480
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GnomAD4 genome ? AF: 0.131 AC: 19846AN: 151736Hom.: 1506 Cov.: 31 AF XY: 0.132 AC XY: 9761AN XY: 74138
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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