chr13-28659090-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000689222.1(ENSG00000289569):n.2G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,547,944 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000085 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000059 ( 0 hom. )
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 3.10
Genes affected
POMP (HGNC:20330): (proteasome maturation protein) The protein encoded by this gene is a molecular chaperone that binds 20S preproteasome components and is essential for 20S proteasome formation. The 20S proteasome is the proteolytically active component of the 26S proteasome complex. The encoded protein is degraded before the maturation of the 20S proteasome is complete. A variant in the 5' UTR of this gene has been associated with KLICK syndrome, a rare skin disorder.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.11).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMP | NM_015932.6 | upstream_gene_variant | ENST00000380842.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000689222.1 | n.2G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
POMP | ENST00000380842.5 | upstream_gene_variant | 1 | NM_015932.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152210Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.0000595 AC: 83AN: 1395616Hom.: 0 Cov.: 29 AF XY: 0.0000581 AC XY: 40AN XY: 688946
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GnomAD4 genome AF: 0.0000853 AC: 13AN: 152328Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74486
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2023 | This variant occurs in a non-coding region of the POMP gene. It does not change the encoded amino acid sequence of the POMP protein. This variant is present in population databases (rs547781197, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with POMP-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at