2-25161283-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000939.4(POMC):c.602C>T(p.Ala201Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000739 in 1,611,110 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_000939.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMC | NM_000939.4 | c.602C>T | p.Ala201Val | missense_variant | 3/3 | ENST00000395826.7 | |
POMC | NM_001035256.3 | c.602C>T | p.Ala201Val | missense_variant | 4/4 | ||
POMC | NM_001319204.2 | c.602C>T | p.Ala201Val | missense_variant | 4/4 | ||
POMC | NM_001319205.2 | c.602C>T | p.Ala201Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMC | ENST00000395826.7 | c.602C>T | p.Ala201Val | missense_variant | 3/3 | 2 | NM_000939.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000291 AC: 7AN: 240824Hom.: 0 AF XY: 0.0000381 AC XY: 5AN XY: 131196
GnomAD4 exome AF: 0.0000740 AC: 108AN: 1459038Hom.: 0 Cov.: 32 AF XY: 0.0000717 AC XY: 52AN XY: 725664
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
POMC-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 20, 2023 | The POMC c.602C>T variant is predicted to result in the amino acid substitution p.Ala201Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0048% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at