4-67581531-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_012108.4(STAP1):c.530+60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,537,914 control chromosomes in the GnomAD database, including 38,752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3171 hom., cov: 33)
Exomes 𝑓: 0.22 ( 35581 hom. )
Consequence
STAP1
NM_012108.4 intron
NM_012108.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.308
Genes affected
STAP1 (HGNC:24133): (signal transducing adaptor family member 1) The protein encoded by this gene contains a proline-rich region, a pleckstrin homology (PH) domain, and a region in the carboxy terminal half with similarity to the Src Homology 2 (SH2) domain. This protein is a substrate of tyrosine-protein kinase Tec, and its interaction with tyrosine-protein kinase Tec is phosphorylation-dependent. This protein is thought to participate in a positive feedback loop by upregulating the activity of tyrosine-protein kinase Tec. Variants of this gene have been associated with autosomal-dominant hypercholesterolemia (ADH), which is characterized by elevated low-density lipoprotein cholesterol levels and in increased risk of coronary vascular disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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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=-0.64).
BP6
?
Variant 4-67581531-A-G is Benign according to our data. Variant chr4-67581531-A-G is described in ClinVar as [Benign]. Clinvar id is 1262529.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAP1 | NM_012108.4 | c.530+60A>G | intron_variant | ENST00000265404.7 | |||
STAP1 | NM_001317769.2 | c.530+60A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAP1 | ENST00000265404.7 | c.530+60A>G | intron_variant | 1 | NM_012108.4 | P1 | |||
STAP1 | ENST00000396225.1 | c.530+60A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.198 AC: 30072AN: 152056Hom.: 3176 Cov.: 33
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GnomAD4 exome AF: 0.223 AC: 309202AN: 1385740Hom.: 35581 AF XY: 0.226 AC XY: 154373AN XY: 683322
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GnomAD4 genome ? AF: 0.198 AC: 30060AN: 152174Hom.: 3171 Cov.: 33 AF XY: 0.202 AC XY: 15049AN XY: 74396
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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 | Apr 14, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at