6-32038610-A-T

Position:

• chr6-32038610-A-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BS1_Supporting

The NM_000500.9(CYP21A2):​c.188A>T​(p.His63Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00971 in 145,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0097 (0 hom., cov: 28)
  • Exomes 𝑓: 0.031 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYP21A2 NM_000500.9 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 B:3
• Conservation: PhyloP100: -0.135

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]

CYP21A2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Variant has high frequency in the EAS(0.0890682) population. However there is too low homozygotes in high coverage region: (expected more than 3, got 0).
• BP4: Computational evidence support a benign effect (MetaRNN=0.0039593577).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00971 (1416/145832) while in subpopulation EAS AF= 0.0497 (204/4104). AF 95% confidence interval is 0.0441. There are 0 homozygotes in gnomad4. There are 720 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A2	NM_000500.9	c.188A>T	p.His63Leu	missense_variant	1/10	ENST00000644719.2	NP_000491.4
CYP21A2	NM_001128590.4	c.188A>T	p.His63Leu	missense_variant	1/9		NP_001122062.3
CYP21A2	NM_001368143.2	c.-237A>T		5_prime_UTR_variant	1/10		NP_001355072.1
CYP21A2	NM_001368144.2	c.-147A>T		5_prime_UTR_variant	1/9		NP_001355073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP21A2	ENST00000644719.2	c.188A>T	p.His63Leu	missense_variant	1/10		NM_000500.9	ENSP00000496625.1

Frequencies

GnomAD3 genomes AF: 0.00970 AC: 1413 AN: 145720 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00211

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0123

Gnomad ASJ AF: 0.00351

Gnomad EAS AF: 0.0496

Gnomad SAS AF: 0.00557

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0139

GnomAD3 exomes AF: 0.0441 AC: 7165 AN: 162570 Hom.: 0 AF XY: 0.0426 AC XY: 3739 AN XY: 87846

Gnomad AFR exome AF: 0.00571

Gnomad AMR exome AF: 0.0632

Gnomad ASJ exome AF: 0.0153

Gnomad EAS exome AF: 0.153

Gnomad SAS exome AF: 0.0217

Gnomad FIN exome AF: 0.0431

Gnomad NFE exome AF: 0.0352

Gnomad OTH exome AF: 0.0366

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0310 AC: 43622 AN: 1406546 Hom.: 0 Cov.: 36 AF XY: 0.0304 AC XY: 21222 AN XY: 697948

Gnomad4 AFR exome AF: 0.00397

Gnomad4 AMR exome AF: 0.0553

Gnomad4 ASJ exome AF: 0.0103

Gnomad4 EAS exome AF: 0.0918

Gnomad4 SAS exome AF: 0.0208

Gnomad4 FIN exome AF: 0.0319

Gnomad4 NFE exome AF: 0.0305

Gnomad4 OTH exome AF: 0.0296

GnomAD4 genome AF: 0.00971 AC: 1416 AN: 145832 Hom.: 0 Cov.: 28 AF XY: 0.0101 AC XY: 720 AN XY: 71284

Gnomad4 AFR AF: 0.00210

Gnomad4 AMR AF: 0.0124

Gnomad4 ASJ AF: 0.00351

Gnomad4 EAS AF: 0.0497

Gnomad4 SAS AF: 0.00578

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0138

Alfa AF: 0.0237 Hom.: 0

ExAC AF: 0.0300 AC: 3489

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Benign:1

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 28, 2022	Frequency data for this variant in the general population cannot be distinguished from that of the CYP21P pseudogene, and are therefore uninformative in assessment of variant pathogenicity. In some published literature, this variant is referred to as c.185A>T (p.His62Leu). This variant has been seen in trans with other recessive pathogenic CYP21A2 variants in multiple individuals with congenital and also nonclassic forms of CAH. Assessment of experimental evidence suggests this variant results in abnormal protein function. See PMID: 18319307, 18381579. -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 28, 2022	The variant has been found in at least one symptomatic individual. Functional evidence suggests that this variant may impact protein function. The variant occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and have phenotype known to be consistent with disease. Based on the available information, this variant is classified as pathogenic. -

Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Pathogenic:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2008	- -

Congenital adrenal hyperplasia Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 01, 2022

Variant summary: CYP21A2 c.188A>T (p.His63Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was present at a high frequency in 7520 out of 19,2468 control chromosomes in the gnomAD database, however, the inability of this data to distinguish the occurrence of this variant in the CYP21A1P pseudogene versus the real CYP21A2 gene makes this data unreliable to formulate conclusive opinions. In a cross-sectional review of the literature, c.188A>T has been reported in isolation as a compound heterozygote in trans with other CYP21A2 alleles in individuals affected with non-classic and simple virilizing forms of Congenital Adrenal Hyperplasia (example, Menassa_2008, Taboas_2013, Fernandez_2020, Nagasaki_2009) as well as a complex allele in cis with other putative CYP21A2 alleles (example, Soardi_2008, Liu_2022) and as a non-informative genotype (without a clear second allele specification) (example, Wang_2021, Yoon_2021). At-least one of these studies reports comprehensive genotyping utilizing orthogonal technologies to confirm the allele origin (example, Fernandez_2020). A recent report by the European Molecular Genetics Quality Network (EMQN) describing the best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency lists this variant among those classified as "definitely pathogenic" for a non-classic phenotype (Baumgartner-Parzer_2020). These data indicate that the variant in isolation is likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in variable levels of CYP21A2 enzyme activity depending upon the substrate utilized, namely 17-Hydroxyprogesterone or Progesterone. The reported activities range from one study reporting 70.8% of WT for conversion of 17OHP to 11-deoxycortisol (i.e., a 29.2% reduction in activity) and 66.5% of WT for conversion of Progesterone to 11-Deoxycorticosterone (DOC) (i.e., a 33.5% reduction in activity) with a similar reduction in maximal velocity (Vmax) (72.17% and 69.16% respectively) (Menassa_2008), while another study reporting a more pronounced impact on activity, 44.5% of WT with 17-OHP substrate and 20.7% of WT with Progesterone substrate (Soardi_2008) and a more pronounced impact of maximal velocity (Vmax) (13% and 8.65% respectively). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Feb 23, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.040	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	17
DANN	Benign	0.77
DEOGEN2	Benign	0.066	.;.;.;T;.;.
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.050	N
LIST_S2	Benign	0.80	.;.;T;T;.;.
MetaRNN	Benign	0.0040	T;T;T;T;T;T
MetaSVM	Benign	-0.96	T
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.8	N;.;D;D;N;.
REVEL	Uncertain	0.45
Sift	Benign	0.33	T;.;T;D;T;.
Sift4G	Uncertain	0.041	D;.;D;T;D;.
Polyphen		0.40	B;B;.;.;.;B
Vest4		0.12
MPC		2.3
ClinPred		0.0019	T
GERP RS		-1.8
gMVP		0.60

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: rs9378252; hg19: chr6-32006387; COSMIC: COSV64473007; COSMIC: COSV64473007;