rs773049259
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001244944.2(STEAP2):c.508A>C(p.Asn170His) variant causes a missense change. The variant allele was found at a frequency of 0.000000694 in 1,440,898 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N170D) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
STEAP2
NM_001244944.2 missense
NM_001244944.2 missense
Scores
4
8
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.16
Publications
0 publications found
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 was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1440898Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 715960 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1440898
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
715960
show subpopulations
African (AFR)
AF:
AC:
1
AN:
32336
American (AMR)
AF:
AC:
0
AN:
40246
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24502
East Asian (EAS)
AF:
AC:
0
AN:
39626
South Asian (SAS)
AF:
AC:
0
AN:
82018
European-Finnish (FIN)
AF:
AC:
0
AN:
52754
Middle Eastern (MID)
AF:
AC:
0
AN:
5618
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1104392
Other (OTH)
AF:
AC:
0
AN:
59406
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.;T;.;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D;.;.;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;M;M;M;M;M;.;M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D
Polyphen
1.0, 0.99
.;D;D;.;D;.;D;.
Vest4
0.70, 0.70, 0.68, 0.70
MutPred
Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);
MVP
MPC
0.41
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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