rs10156056

Variant names:

• chr7-22714469-G-C
• rs10156056
• ENST00000650428.1:n.46+13099C>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+13099C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,186 control chromosomes in the GnomAD database, including 2,346 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 0.16 (2346 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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+13099C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24741 AN: 152068 Hom.: 2353 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.163 AC: 24752 AN: 152186 Hom.: 2346 Cov.: 32 AF XY: 0.164 AC XY: 12230 AN XY: 74412

African (AFR) AF: 0.252 AC: 10449 AN: 41498

American (AMR) AF: 0.113 AC: 1729 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.105 AC: 508 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2308 AN: 10598

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8363 AN: 68004

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.157 Hom.: 297

Bravo AF: 0.160

Asia WGS AF: 0.0570 AC: 199 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	0.24
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10156056; hg19: chr7-22754088;