rs17364464

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001382447.1(STEAP1B):​c.762+18131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,236 control chromosomes in the GnomAD database, including 1,216 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 0.12 ( 1216 hom., cov: 32)

Consequence

STEAP1B
NM_001382447.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STEAP1BNM_001382447.1 linkuse as main transcriptc.762+18131T>C intron_variant ENST00000678116.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STEAP1BENST00000678116.1 linkuse as main transcriptc.762+18131T>C intron_variant NM_001382447.1 A2
STEAP1BENST00000404369.8 linkuse as main transcriptc.762+18131T>C intron_variant 1 A2Q6NZ63-2
STEAP1BENST00000406890.6 linkuse as main transcriptc.705+18131T>C intron_variant 1 P2Q6NZ63-1

Frequencies

GnomAD3 genomes
AF:
0.123
AC:
18646
AN:
152118
Hom.:
1210
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0831
Gnomad AMI
AF:
0.174
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.0991
Gnomad EAS
AF:
0.121
Gnomad SAS
AF:
0.110
Gnomad FIN
AF:
0.163
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.102
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.123
AC:
18671
AN:
152236
Hom.:
1216
Cov.:
32
AF XY:
0.122
AC XY:
9106
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0835
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.0991
Gnomad4 EAS
AF:
0.121
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.163
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.140
Hom.:
2361
Bravo
AF:
0.118
Asia WGS
AF:
0.134
AC:
467
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.6
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs17364464; hg19: chr7-22514053; API