15-74343027-C-T

Position:

• chr15-74343027-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The NM_000781.3(CYP11A1):​c.940G>A​(p.Glu314Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 1,613,102 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 0.0025 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0040 (17 hom.)
• Consequence: CYP11A1 NM_000781.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:4 B:3
• Conservation: PhyloP100: 1.95

Genes affected

CYP11A1 (HGNC:2590): (cytochrome P450 family 11 subfamily A member 1) 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 mitochondrial inner membrane and catalyzes the conversion of cholesterol to pregnenolone, the first and rate-limiting step in the synthesis of the steroid hormones. Two transcript variants encoding different isoforms have been found for this gene. The cellular location of the smaller isoform is unclear since it lacks the mitochondrial-targeting transit peptide. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.011359721).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00404 (5906/1460800) while in subpopulation NFE AF= 0.00483 (5375/1111974). AF 95% confidence interval is 0.00473. There are 17 homozygotes in gnomad4_exome. There are 2895 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAdExome4 at 17 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP11A1	NM_000781.3	c.940G>A	p.Glu314Lys	missense_variant	5/9	ENST00000268053.11
CYP11A1	NM_001099773.2	c.466G>A	p.Glu156Lys	missense_variant	5/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP11A1	ENST00000268053.11	c.940G>A	p.Glu314Lys	missense_variant	5/9	1	NM_000781.3	P1
CYP11A1	ENST00000358632.8	c.466G>A	p.Glu156Lys	missense_variant	5/9	2
CYP11A1	ENST00000566674.5	c.466G>A	p.Glu156Lys	missense_variant	5/6	5
CYP11A1	ENST00000435365.5	c.940G>A	p.Glu314Lys	missense_variant, NMD_transcript_variant	5/8	3

Frequencies

GnomAD3 genomes AF: 0.00248 AC: 378 AN: 152184 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000941

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00422

Gnomad OTH AF: 0.00287

GnomAD3 exomes AF: 0.00253 AC: 636 AN: 251458 Hom.: 4 AF XY: 0.00263 AC XY: 358 AN XY: 135902

Gnomad AFR exome AF: 0.000923

Gnomad AMR exome AF: 0.000491

Gnomad ASJ exome AF: 0.000794

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00157

Gnomad FIN exome AF: 0.00222

Gnomad NFE exome AF: 0.00424

Gnomad OTH exome AF: 0.00293

GnomAD4 exome AF: 0.00404 AC: 5906 AN: 1460800 Hom.: 17 Cov.: 32 AF XY: 0.00398 AC XY: 2895 AN XY: 726720

Gnomad4 AFR exome AF: 0.000807

Gnomad4 AMR exome AF: 0.000380

Gnomad4 ASJ exome AF: 0.000650

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00167

Gnomad4 FIN exome AF: 0.00243

Gnomad4 NFE exome AF: 0.00483

Gnomad4 OTH exome AF: 0.00313

GnomAD4 genome AF: 0.00248 AC: 378 AN: 152302 Hom.: 1 Cov.: 32 AF XY: 0.00234 AC XY: 174 AN XY: 74470

Gnomad4 AFR AF: 0.000938

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.00422

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00370 Hom.: 10

Bravo AF: 0.00221

TwinsUK AF: 0.00566 AC: 21

ALSPAC AF: 0.00467 AC: 18

ESP6500AA AF: 0.00182 AC: 8

ESP6500EA AF: 0.00338 AC: 29

ExAC AF: 0.00242 AC: 294

EpiCase AF: 0.00387

EpiControl AF: 0.00350

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:4 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Congenital adrenal insufficiency with 46, XY sex reversal OR 46,XY disorder of sex development-adrenal insufficiency due to CYP11A1 deficiency Pathogenic:2 Uncertain:2 Benign:2

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 10, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	May 19, 2023	PS3, PM3 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jun 30, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 314 of the CYP11A1 protein (p.Glu314Lys). This variant is present in population databases (rs6161, gnomAD 0.4%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with primary adrenal insufficiency (PMID: 30299480, 30620006). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant has only been described in association with primary adrenal insufficiency, when present in trans with another loss of function allele. This variant is not associated with primary adrenal insufficiency when present in the homozygous state. ClinVar contains an entry for this variant (Variation ID: 372354). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The lysine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2016	The E314K variant has been reported previously in two unrelated individuals with primary adrenal insufficiency; one individual harbored another CYP11A1 variant in trans whereas the other reported individual had no other molecular findings (Chan et al., 2015). Although not present in the homozygous state, the NHLBI ESP Exome Sequencing Project reports E314K was observed in 0.34% (29/8,592) alleles from individuals of European American ancestry. The E314K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The E314K variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded. -

not specified Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 09, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 07, 2023	Variant summary: CYP11A1 c.940G>A (p.Glu314Lys) results in a 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. At least one publication reports experimental evidence that this variant affects mRNA splicing. The variant allele was found at a frequency of 0.0025 in 251458 control chromosomes, including 4 homozygotes, and is found predominantly at a frequency of 0.0042 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 4.6 fold of the estimated maximal expected allele frequency for a pathogenic variant in CYP11A1 causing Congenital Adrenal Hyperplasia phenotype (0.00091), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. However, the inability of this data to distinguish the occurrence of this variant in a pseudogene versus the real CYP11A1 gene makes this data unreliable to formulate conclusive opinions. c.940G>A has been reported in the literature in the compound heterozygous state in individuals affected with Adrenal Insufficiency, including multiple cases where it has been reported in trans with a pathogenic variant and in families where it was reported to segregate with the disease phenotype (e.g. Chan_2015, Goursaud_2018, Maharaj_2019, Kolli_2019a), suggesting that the variant is very likely to be associated with disease. To our knowledge, the variant has not been reported in the homozygous state in affected individuals. Several publications report experimental evidence evaluating an impact on protein function (e.g. Goursaud_2018, Maharaj_2019, Kolli_2019a). Minigene assays have indicated that the variant affects mRNA splicing, resulting in the skipping of exon 5, which would result in a frameshift leading to a premature termination codon, and analysis of mRNA from an individual with the variant showed that this occurred in a larger proportion of transcripts than in a control individual, but that not all transcripts were affected. Enzyme activity assays have provided mixed results regarding the variant effect on protein function. Expression of the purified E314K variant protein in Ecoli and expression in COS1 cells showed comparable activity to the WT protein. However, it exhibited reduced protein expression/stability in HEK-293 cells, with approximately 60% activity compared to WT and in V9 cells, enzyme activity was undetectable. The following publications have been ascertained in the context of this evaluation (PMID: 26300845, 30233493, 30299480, 30620006). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, classifying the variant as pathogenic (n=1)/likely pathogenic (n=3), benign (n=1)/likely benign (n=2) or VUS (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -

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

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Apr 04, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.43	.;T;.
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.66
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.86	D;D;D
M_CAP	Benign	0.079	D
MetaRNN	Benign	0.011	T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.30	.;N;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-3.3	D;D;D
REVEL	Benign	0.13
Sift	Benign	0.10	T;T;T
Sift4G	Benign	0.34	T;T;.
Polyphen		0.063	.;B;.
Vest4		0.31
MVP		0.79
MPC		0.41
ClinPred		1.0	D
GERP RS		1.4
Varity_R		0.55
gMVP		0.55

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: rs6161; hg19: chr15-74635368; COSMIC: COSV51430586; COSMIC: COSV51430586;