8-142872874-G-A

Variant names:

• chr8-142872874-G-A
• rs1134095
• NM_000497.4:c.*1499C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000497.4(CYP11B1):​c.*1499C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,014 control chromosomes in the GnomAD database, including 28,976 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.61 (28974 hom., cov: 31)
  • Exomes 𝑓: 0.58 (2 hom.)
• Consequence: CYP11B1 NM_000497.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.709
• Publications: 17 publications found

Genes affected

CYP11B1 (HGNC:2591): (cytochrome P450 family 11 subfamily B 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 is involved in the conversion of progesterone to cortisol in the adrenal cortex. Mutations in this gene cause congenital adrenal hyperplasia due to 11-beta-hydroxylase deficiency. Transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]

GML (HGNC:4375): (glycosylphosphatidylinositol anchored molecule like) Predicted to be involved in DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; apoptotic process; and negative regulation of cell population proliferation. Predicted to be extrinsic component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 8-142872874-G-A is Benign according to our data. Variant chr8-142872874-G-A is described in ClinVar as [Benign]. Clinvar id is 362111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP11B1	NM_000497.4	c.*1499C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000292427.10	NP_000488.3
CYP11B1	NM_001026213.1	c.*1499C>T		3_prime_UTR_variant	Exon 8 of 8		NP_001021384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP11B1	ENST00000292427.10	c.*1499C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_000497.4	ENSP00000292427.5
CYP11B1	ENST00000519285.5	c.*1499C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000430144.1
CYP11B1	ENST00000314111.4	n.3208C>T		non_coding_transcript_exon_variant	Exon 7 of 7	5
GML	ENST00000522728.5	c.181+31649G>A		intron_variant	Intron 3 of 4	3		ENSP00000430799.1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93296 AN: 151884 Hom.: 28954 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.600 AC: 6 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.614 AC: 93366 AN: 152002 Hom.: 28974 Cov.: 31 AF XY: 0.622 AC XY: 46222 AN XY: 74270

African (AFR) AF: 0.640 AC: 26515 AN: 41444

American (AMR) AF: 0.636 AC: 9714 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2248 AN: 3472

East Asian (EAS) AF: 0.847 AC: 4373 AN: 5164

South Asian (SAS) AF: 0.739 AC: 3556 AN: 4810

European-Finnish (FIN) AF: 0.612 AC: 6463 AN: 10554

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38481 AN: 67978

Other (OTH) AF: 0.625 AC: 1314 AN: 2102

Alfa AF: 0.586 Hom.: 78882

Bravo AF: 0.613

Asia WGS AF: 0.729 AC: 2535 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Deficiency of steroid 11-beta-monooxygenase Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Glucocorticoid-remediable aldosteronism Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1134095; hg19: chr8-143954290;