rs11563929
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000394621.7(STEAP2):c.*4907G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 152,934 control chromosomes in the GnomAD database, including 154 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.016 ( 154 hom., cov: 32)
Exomes 𝑓: 0.012 ( 0 hom. )
Consequence
STEAP2
ENST00000394621.7 3_prime_UTR
ENST00000394621.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.547
Genes affected
STEAP2 (HGNC:17885): (STEAP2 metalloreductase) This gene is a member of the STEAP family and encodes a multi-pass membrane protein that localizes to the Golgi complex, the plasma membrane, and the vesicular tubular structures in the cytosol. A highly similar protein in mouse has both ferrireductase and cupric reductase activity, and stimulates the cellular uptake of both iron and copper in vitro. Increased transcriptional expression of the human gene is associated with prostate cancer progression. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STEAP2 | NM_001244944.2 | c.*4907G>T | 3_prime_UTR_variant | 6/6 | ENST00000394621.7 | NP_001231873.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STEAP2 | ENST00000394621.7 | c.*4907G>T | 3_prime_UTR_variant | 6/6 | 1 | NM_001244944.2 | ENSP00000378119 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 2470AN: 151976Hom.: 154 Cov.: 32
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GnomAD4 exome AF: 0.0119 AC: 10AN: 840Hom.: 0 Cov.: 0 AF XY: 0.0114 AC XY: 5AN XY: 440
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GnomAD4 genome AF: 0.0163 AC: 2475AN: 152094Hom.: 154 Cov.: 32 AF XY: 0.0190 AC XY: 1413AN XY: 74344
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ClinVar
Not reported inComputational 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