rs6468

chr6-32038540-C-Gchr6-32038540-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_000500.9(CYP21A2):c.118C>G(p.Leu40Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L40L) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000028 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYP21A2 NM_000500.9 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.41448003).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP21A2	NM_000500.9	c.118C>G	p.Leu40Val	missense_variant	1/10	ENST00000644719.2
CYP21A2	NM_001128590.4	c.118C>G	p.Leu40Val	missense_variant	1/9
CYP21A2	NM_001368143.2	c.-307C>G		5_prime_UTR_variant	1/10
CYP21A2	NM_001368144.2	c.-217C>G		5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP21A2	ENST00000644719.2	c.118C>G	p.Leu40Val	missense_variant	1/10		NM_000500.9	P1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000276 AC: 4 AN: 1451672 Hom.: 0 Cov.: 121 AF XY: 0.00000139 AC XY: 1 AN XY: 721310

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000361

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.024	T
BayesDel_noAF	Benign	-0.27
Cadd	Benign	18
Dann	Uncertain	0.98
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.36
FATHMM_MKL	Uncertain	0.82	D
M_CAP	Pathogenic	0.58	D
MetaRNN	Benign	0.41	T;T;T;T;T;T
MetaSVM	Benign	-0.50	T
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-1.4	N;.;N;N;N;.
REVEL	Uncertain	0.36
Sift	Uncertain	0.011	D;.;D;D;D;.
Sift4G	Uncertain	0.023	D;.;T;T;D;.
Polyphen		0.98	D;D;.;.;.;D
Vest4		0.21
MutPred		0.49		Gain of catalytic residue at Q42 (P = 0.091);Gain of catalytic residue at Q42 (P = 0.091);Gain of catalytic residue at Q42 (P = 0.091);Gain of catalytic residue at Q42 (P = 0.091);Gain of catalytic residue at Q42 (P = 0.091);Gain of catalytic residue at Q42 (P = 0.091);
MVP		0.83
MPC		3.4
ClinPred		0.72	D
GERP RS		0.64
gMVP		0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6468; hg19: chr6-32006317;