2-25164312-T-G

Position:

• chr2-25164312-T-G

Variant summary

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

The NM_000939.4(POMC):​c.132+329A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,002 control chromosomes in the GnomAD database, including 5,563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5563 hom., cov: 32)
• Consequence: POMC NM_000939.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.10

Genes affected

POMC (HGNC:9201): (proopiomelanocortin) This gene encodes a preproprotein that undergoes extensive, tissue-specific, post-translational processing via cleavage by subtilisin-like enzymes known as prohormone convertases. There are eight potential cleavage sites within the preproprotein and, depending on tissue type and the available convertases, processing may yield as many as ten biologically active peptides involved in diverse cellular functions. The encoded protein is synthesized mainly in corticotroph cells of the anterior pituitary where four cleavage sites are used; adrenocorticotrophin, essential for normal steroidogenesis and the maintenance of normal adrenal weight, and lipotropin beta are the major end products. In other tissues, including the hypothalamus, placenta, and epithelium, all cleavage sites may be used, giving rise to peptides with roles in pain and energy homeostasis, melanocyte stimulation, and immune modulation. These include several distinct melanotropins, lipotropins, and endorphins that are contained within the adrenocorticotrophin and beta-lipotropin peptides. The antimicrobial melanotropin alpha peptide exhibits antibacterial and antifungal activity. Mutations in this gene have been associated with early onset obesity, adrenal insufficiency, and red hair pigmentation. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 2-25164312-T-G is Benign according to our data. Variant chr2-25164312-T-G is described in ClinVar as [Benign]. Clinvar id is 1258300.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POMC	NM_000939.4	c.132+329A>C		intron_variant		ENST00000395826.7	NP_000930.1
POMC	NM_001035256.3	c.132+329A>C		intron_variant			NP_001030333.1
POMC	NM_001319204.2	c.132+329A>C		intron_variant			NP_001306133.1
POMC	NM_001319205.2	c.132+329A>C		intron_variant			NP_001306134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POMC	ENST00000395826.7	c.132+329A>C		intron_variant		2	NM_000939.4	ENSP00000379170.2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37682 AN: 151884 Hom.: 5546 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.234

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.248 AC: 37714 AN: 152002 Hom.: 5563 Cov.: 32 AF XY: 0.265 AC XY: 19696 AN XY: 74320

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.234

Alfa AF: 0.228 Hom.: 493

Bravo AF: 0.248

Asia WGS AF: 0.448 AC: 1558 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.3
DANN	Benign	0.58

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: rs12473543; hg19: chr2-25387181;