GeneBe

ENST00000650428.1:n.46+9684G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000650428.1(STEAP1B):​n.46+9684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,020 control chromosomes in the GnomAD database, including 27,858 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 0.59 ( 27858 hom., cov: 32)

Consequence

STEAP1B
ENST00000650428.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.468

Publications

8 publications found
Variant links:
Genes affected
STEAP1B (HGNC:41907): (STEAP family member 1B) Predicted to be integral component of membrane. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STEAP1BENST00000650428.1 linkn.46+9684G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.588
AC:
89307
AN:
151902
Hom.:
27836
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.797
Gnomad AMI
AF:
0.515
Gnomad AMR
AF:
0.580
Gnomad ASJ
AF:
0.631
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.457
Gnomad FIN
AF:
0.440
Gnomad MID
AF:
0.728
Gnomad NFE
AF:
0.519
Gnomad OTH
AF:
0.603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.588
AC:
89390
AN:
152020
Hom.:
27858
Cov.:
32
AF XY:
0.583
AC XY:
43312
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.796
AC:
33021
AN:
41468
American (AMR)
AF:
0.580
AC:
8860
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.631
AC:
2187
AN:
3464
East Asian (EAS)
AF:
0.242
AC:
1254
AN:
5176
South Asian (SAS)
AF:
0.456
AC:
2199
AN:
4818
European-Finnish (FIN)
AF:
0.440
AC:
4638
AN:
10532
Middle Eastern (MID)
AF:
0.731
AC:
215
AN:
294
European-Non Finnish (NFE)
AF:
0.519
AC:
35273
AN:
67960
Other (OTH)
AF:
0.603
AC:
1273
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1715
3430
5145
6860
8575
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
726
1452
2178
2904
3630
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.570
Hom.:
4787
Bravo
AF:
0.612
Asia WGS
AF:
0.394
AC:
1368
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.2
DANN
Benign
0.78
PhyloP100
0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1546762; hg19: chr7-22757503; API