chr6-32040674-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000500.9(CYP21A2):c.1125C>T(p.Ser375=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 146,200 control chromosomes in the GnomAD database, including 439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S375S) has been classified as Likely benign.
Frequency
Consequence
NM_000500.9 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP21A2 | NM_000500.9 | c.1125C>T | p.Ser375= | synonymous_variant | 9/10 | ENST00000644719.2 | |
CYP21A2 | NM_001128590.4 | c.1035C>T | p.Ser345= | synonymous_variant | 8/9 | ||
CYP21A2 | NM_001368143.2 | c.720C>T | p.Ser240= | synonymous_variant | 9/10 | ||
CYP21A2 | NM_001368144.2 | c.720C>T | p.Ser240= | synonymous_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP21A2 | ENST00000644719.2 | c.1125C>T | p.Ser375= | synonymous_variant | 9/10 | NM_000500.9 | P1 |
Frequencies
GnomAD3 genomes AF: 0.166 AC: 24206AN: 146080Hom.: 441 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.164 AC: 228468AN: 1390034Hom.: 3961 Cov.: 34 AF XY: 0.164 AC XY: 113449AN XY: 691930
GnomAD4 genome AF: 0.166 AC: 24235AN: 146200Hom.: 439 Cov.: 33 AF XY: 0.166 AC XY: 11866AN XY: 71394
ClinVar
Submissions by phenotype
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 | GeneDx | May 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at