18-13882740-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000529.2(MC2R):c.*1885T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 152,336 control chromosomes in the GnomAD database, including 751 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.080 (751 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: MC2R NM_000529.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.681

Genes affected

MC2R (HGNC:6930): (melanocortin 2 receptor) MC2R encodes one member of the five-member G-protein associated melanocortin receptor family. Melanocortins (melanocyte-stimulating hormones and adrenocorticotropic hormone) are peptides derived from pro-opiomelanocortin (POMC). MC2R is selectively activated by adrenocorticotropic hormone, whereas the other four melanocortin receptors recognize a variety of melanocortin ligands. Mutations in MC2R can result in familial glucocorticoid deficiency. Alternate transcript variants have been found for this gene. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 18-13882740-A-G is Benign according to our data. Variant chr18-13882740-A-G is described in ClinVar as [Benign]. Clinvar id is 326133.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MC2R	NM_000529.2	c.*1885T>C		3_prime_UTR_variant	2/2	ENST00000327606.4
MC2R	NM_001291911.1	c.*1885T>C		3_prime_UTR_variant	2/2
MC2R	XM_017025781.2	c.*1885T>C		3_prime_UTR_variant	3/3
MC2R	XM_047437537.1	c.*1885T>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MC2R	ENST00000327606.4	c.*1885T>C		3_prime_UTR_variant	2/2	1	NM_000529.2	P1

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12097 AN: 152218 Hom.: 749 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0664

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0796 AC: 12128 AN: 152336 Hom.: 751 Cov.: 33 AF XY: 0.0806 AC XY: 6000 AN XY: 74486

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0183

Gnomad4 NFE AF: 0.0336

Gnomad4 OTH AF: 0.0671

Alfa AF: 0.0521 Hom.: 59

Bravo AF: 0.0895

Asia WGS AF: 0.119 AC: 411 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Glucocorticoid deficiency 1 Benign:1

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 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	-0.90
Cadd	Benign	1.3
Dann	Benign	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: rs3760536; hg19: chr18-13882739;