rs6474
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000500.9(CYP21A2):c.308G>A(p.Arg103Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,595,216 control chromosomes in the GnomAD database, including 79,844 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000500.9 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP21A2 | NM_000500.9 | c.308G>A | p.Arg103Lys | missense_variant | 3/10 | ENST00000644719.2 | |
CYP21A2 | NM_001128590.4 | c.218G>A | p.Arg73Lys | missense_variant | 2/9 | ||
CYP21A2 | NM_001368143.2 | c.-98G>A | 5_prime_UTR_variant | 3/10 | |||
CYP21A2 | NM_001368144.2 | c.-98G>A | 5_prime_UTR_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP21A2 | ENST00000644719.2 | c.308G>A | p.Arg103Lys | missense_variant | 3/10 | NM_000500.9 | P1 |
Frequencies
GnomAD3 genomes AF: 0.257 AC: 38624AN: 150542Hom.: 6397 Cov.: 30
GnomAD3 exomes AF: 0.316 AC: 75713AN: 239240Hom.: 13678 AF XY: 0.314 AC XY: 40568AN XY: 129016
GnomAD4 exome AF: 0.310 AC: 447411AN: 1444554Hom.: 73438 Cov.: 83 AF XY: 0.310 AC XY: 222057AN XY: 717456
GnomAD4 genome AF: 0.256 AC: 38642AN: 150662Hom.: 6406 Cov.: 30 AF XY: 0.261 AC XY: 19189AN XY: 73518
ClinVar
Submissions by phenotype
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Benign:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at