GeneBe

ENST00000650428.1:n.46+34218C>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+34218C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,938 control chromosomes in the GnomAD database, including 60,839 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 0.89 ( 60839 hom., cov: 28)

Consequence

STEAP1B
ENST00000650428.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

5 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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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+34218C>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.886
AC:
134515
AN:
151822
Hom.:
60802
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.881
Gnomad AMI
AF:
0.980
Gnomad AMR
AF:
0.812
Gnomad ASJ
AF:
0.917
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.690
Gnomad FIN
AF:
0.942
Gnomad MID
AF:
0.934
Gnomad NFE
AF:
0.951
Gnomad OTH
AF:
0.874
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.886
AC:
134605
AN:
151938
Hom.:
60839
Cov.:
28
AF XY:
0.879
AC XY:
65261
AN XY:
74282
show subpopulations
African (AFR)
AF:
0.881
AC:
36477
AN:
41412
American (AMR)
AF:
0.812
AC:
12369
AN:
15236
Ashkenazi Jewish (ASJ)
AF:
0.917
AC:
3179
AN:
3468
East Asian (EAS)
AF:
0.315
AC:
1620
AN:
5150
South Asian (SAS)
AF:
0.690
AC:
3312
AN:
4800
European-Finnish (FIN)
AF:
0.942
AC:
9963
AN:
10574
Middle Eastern (MID)
AF:
0.925
AC:
272
AN:
294
European-Non Finnish (NFE)
AF:
0.951
AC:
64680
AN:
67984
Other (OTH)
AF:
0.873
AC:
1841
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
657
1314
1970
2627
3284
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
880
1760
2640
3520
4400
<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:
0.920
Hom.:
31975
Bravo
AF:
0.878
Asia WGS
AF:
0.557
AC:
1943
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.3
DANN
Benign
0.68
PhyloP100
0.049

Splicing

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

Publications

Other links and lift over

dbSNP: rs2106549; hg19: chr7-22732969; API