rs6664294
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005857.5(ZMPSTE24):c.1204-124T>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 873,268 control chromosomes in the GnomAD database, including 27,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 4829 hom., cov: 32)
Exomes 𝑓: 0.25 ( 22761 hom. )
Consequence
ZMPSTE24
NM_005857.5 intron
NM_005857.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0570
Genes affected
ZMPSTE24 (HGNC:12877): (zinc metallopeptidase STE24) This gene encodes a member of the peptidase M48A family. The encoded protein is a zinc metalloproteinase involved in the two step post-translational proteolytic cleavage of carboxy terminal residues of farnesylated prelamin A to form mature lamin A. Mutations in this gene have been associated with mandibuloacral dysplasia and restrictive dermopathy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 1-40292321-T-C is Benign according to our data. Variant chr1-40292321-T-C is described in ClinVar as [Benign]. Clinvar id is 1260900.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMPSTE24 | NM_005857.5 | c.1204-124T>C | intron_variant | ENST00000372759.4 | |||
ZMPSTE24 | XM_047427582.1 | c.955-124T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMPSTE24 | ENST00000372759.4 | c.1204-124T>C | intron_variant | 1 | NM_005857.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.249 AC: 37783AN: 151964Hom.: 4828 Cov.: 32
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GnomAD4 exome AF: 0.249 AC: 179224AN: 721184Hom.: 22761 AF XY: 0.244 AC XY: 93756AN XY: 383682
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GnomAD4 genome ? AF: 0.248 AC: 37779AN: 152084Hom.: 4829 Cov.: 32 AF XY: 0.248 AC XY: 18400AN XY: 74334
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at