rs397515531
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBS2_Supporting
The NM_000500.9(CYP21A2):āc.552C>Gā(p.Asp184Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,580,942 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000500.9 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP21A2 | NM_000500.9 | c.552C>G | p.Asp184Glu | missense_variant, splice_region_variant | 5/10 | ENST00000644719.2 | |
CYP21A2 | NM_001128590.4 | c.462C>G | p.Asp154Glu | missense_variant, splice_region_variant | 4/9 | ||
CYP21A2 | NM_001368143.2 | c.147C>G | p.Asp49Glu | missense_variant, splice_region_variant | 5/10 | ||
CYP21A2 | NM_001368144.2 | c.147C>G | p.Asp49Glu | missense_variant, splice_region_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP21A2 | ENST00000644719.2 | c.552C>G | p.Asp184Glu | missense_variant, splice_region_variant | 5/10 | NM_000500.9 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00300 AC: 453AN: 150816Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00145 AC: 308AN: 211870Hom.: 12 AF XY: 0.00136 AC XY: 155AN XY: 113944
GnomAD4 exome AF: 0.00197 AC: 2812AN: 1430014Hom.: 48 Cov.: 58 AF XY: 0.00200 AC XY: 1419AN XY: 708910
GnomAD4 genome ? AF: 0.00301 AC: 455AN: 150928Hom.: 2 Cov.: 31 AF XY: 0.00294 AC XY: 217AN XY: 73740
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CYP21A2: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 05, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at