rs7805828

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+8625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,974 control chromosomes in the GnomAD database, including 11,593 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 0.39 ( 11593 hom., cov: 32)

Consequence

STEAP1B
ENST00000650428.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.390
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 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+8625C>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58994
AN:
151856
Hom.:
11581
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.382
Gnomad AMI
AF:
0.367
Gnomad AMR
AF:
0.431
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.312
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.415
Gnomad OTH
AF:
0.406
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59047
AN:
151974
Hom.:
11593
Cov.:
32
AF XY:
0.383
AC XY:
28416
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.382
AC:
0.382435
AN:
0.382435
Gnomad4 AMR
AF:
0.431
AC:
0.43105
AN:
0.43105
Gnomad4 ASJ
AF:
0.393
AC:
0.392734
AN:
0.392734
Gnomad4 EAS
AF:
0.238
AC:
0.2385
AN:
0.2385
Gnomad4 SAS
AF:
0.312
AC:
0.312007
AN:
0.312007
Gnomad4 FIN
AF:
0.283
AC:
0.283425
AN:
0.283425
Gnomad4 NFE
AF:
0.415
AC:
0.415347
AN:
0.415347
Gnomad4 OTH
AF:
0.409
AC:
0.409091
AN:
0.409091
Heterozygous variant carriers
0
1851
3702
5552
7403
9254
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
554
1108
1662
2216
2770
<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:
0.402
Hom.:
21347
Bravo
AF:
0.401
Asia WGS
AF:
0.308
AC:
1070
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.3
DANN
Benign
0.66

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7805828; hg19: chr7-22758562; API