rs10499563

Variant names:

• chr7-22720869-T-C
• rs10499563
• ENST00000650428.1:n.46+6699A>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+6699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,134 control chromosomes in the GnomAD database, including 3,329 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 0.21 (3329 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 90 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650428.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000650428.1		n.46+6699A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31647 AN: 152016 Hom.: 3324 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.208 AC: 31665 AN: 152134 Hom.: 3329 Cov.: 32 AF XY: 0.207 AC XY: 15368 AN XY: 74368

African (AFR) AF: 0.207 AC: 8608 AN: 41508

American (AMR) AF: 0.200 AC: 3056 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3468

East Asian (EAS) AF: 0.176 AC: 910 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10590

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14971 AN: 67972

Other (OTH) AF: 0.239 AC: 504 AN: 2108

Alfa AF: 0.217 Hom.: 9318

Bravo AF: 0.213

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.53
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10499563; hg19: chr7-22760488;