chr7-90225570-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001244944.2(STEAP2):c.488G>A(p.Arg163Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000303 in 1,584,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R163W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001244944.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STEAP2 | NM_001244944.2 | c.488G>A | p.Arg163Gln | missense_variant | 3/6 | ENST00000394621.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STEAP2 | ENST00000394621.7 | c.488G>A | p.Arg163Gln | missense_variant | 3/6 | 1 | NM_001244944.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000314 AC: 7AN: 222606Hom.: 0 AF XY: 0.0000332 AC XY: 4AN XY: 120494
GnomAD4 exome AF: 0.0000202 AC: 29AN: 1432306Hom.: 0 Cov.: 33 AF XY: 0.0000169 AC XY: 12AN XY: 710656
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2022 | The c.488G>A (p.R163Q) alteration is located in exon 2 (coding exon 1) of the STEAP2 gene. This alteration results from a G to A substitution at nucleotide position 488, causing the arginine (R) at amino acid position 163 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at