rs17147230

Variant names:

• chr7-22722557-T-A
• rs17147230
• ENST00000650428.1:n.46+5011A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22722557-T-A
• chr7-22722557-T-C
• chr7-22722557-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650428.1(STEAP1B):​n.46+5011A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,274 control chromosomes in the GnomAD database, including 1,067 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 0.040 (1067 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 16 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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
STEAP1B	ENST00000650428.1	n.46+5011A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6068 AN: 152156 Hom.: 1068 Cov.: 32

Gnomad AFR AF: 0.00574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00118

Gnomad OTH AF: 0.0345

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0399 AC: 6069 AN: 152274 Hom.: 1067 Cov.: 32 AF XY: 0.0480 AC XY: 3570 AN XY: 74450

African (AFR) AF: 0.00573 AC: 238 AN: 41558

American (AMR) AF: 0.100 AC: 1537 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2864 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4812

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00118 AC: 80 AN: 68022

Other (OTH) AF: 0.0370 AC: 78 AN: 2110

Alfa AF: 0.0141 Hom.: 20

Bravo AF: 0.0446

Asia WGS AF: 0.331 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs17147230; hg19: chr7-22762176;