rs10155981

Variant names:

• chr7-22716844-C-T
• rs10155981
• ENST00000650428.1:n.46+10724G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650428.1(STEAP1B):​n.46+10724G>A 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 150,232 control chromosomes in the GnomAD database, including 4,981 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 (4981 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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+10724G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31277 AN: 150158 Hom.: 4975 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00254

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.208 AC: 31318 AN: 150232 Hom.: 4981 Cov.: 31 AF XY: 0.209 AC XY: 15313 AN XY: 73160

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.00255

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.198

Alfa AF: 0.126 Hom.: 1364

Bravo AF: 0.220

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10155981; hg19: chr7-22756463;