rs708670
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_182915.3(STEAP3):c.-393-959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,040 control chromosomes in the GnomAD database, including 9,876 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 0.35 ( 9876 hom., cov: 32)
Consequence
STEAP3
NM_182915.3 intron
NM_182915.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.722
Genes affected
STEAP3 (HGNC:24592): (STEAP3 metalloreductase) This gene encodes a multipass membrane protein that functions as an iron transporter. The encoded protein can reduce both iron (Fe3+) and copper (Cu2+) cations. This protein may mediate downstream responses to p53, including promoting apoptosis. Deficiency in this gene can cause anemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STEAP3 | NM_182915.3 | c.-393-959G>A | intron_variant | ENST00000393110.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STEAP3 | ENST00000393110.7 | c.-393-959G>A | intron_variant | 1 | NM_182915.3 | ||||
STEAP3 | ENST00000393106.6 | c.-77+5773G>A | intron_variant | 1 | P1 | ||||
STEAP3 | ENST00000393107.2 | c.-9+5773G>A | intron_variant | 1 | P1 | ||||
STEAP3 | ENST00000409811.5 | c.-9+5773G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.354 AC: 53835AN: 151924Hom.: 9866 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.354 AC: 53873AN: 152040Hom.: 9876 Cov.: 32 AF XY: 0.348 AC XY: 25865AN XY: 74330
GnomAD4 genome
?
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25865
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1002
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at