chr2-25161087-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000939.4(POMC):c.798C>T(p.Gly266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
POMC
NM_000939.4 synonymous
NM_000939.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.26
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 2-25161087-G-A is Benign according to our data. Variant chr2-25161087-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1567506.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.26 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMC | NM_000939.4 | c.798C>T | p.Gly266= | synonymous_variant | 3/3 | ENST00000395826.7 | |
POMC | NM_001035256.3 | c.798C>T | p.Gly266= | synonymous_variant | 4/4 | ||
POMC | NM_001319204.2 | c.798C>T | p.Gly266= | synonymous_variant | 4/4 | ||
POMC | NM_001319205.2 | c.798C>T | p.Gly266= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMC | ENST00000395826.7 | c.798C>T | p.Gly266= | synonymous_variant | 3/3 | 2 | NM_000939.4 | P1 | |
POMC | ENST00000405623.5 | c.798C>T | p.Gly266= | synonymous_variant | 3/3 | 1 | P1 | ||
POMC | ENST00000264708.7 | c.798C>T | p.Gly266= | synonymous_variant | 4/4 | 2 | P1 | ||
POMC | ENST00000380794.5 | c.798C>T | p.Gly266= | synonymous_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251044Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135796
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461806Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727210
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 02, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at