ENST00000650428.1:n.47-40336C>T

Variant names:

• chr7-22673258-G-A
• rs2905325
• ENST00000650428.1:n.47-40336C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.47-40336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,234 control chromosomes in the GnomAD database, including 59,445 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 0.87 (59445 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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.47-40336C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 133021 AN: 152116 Hom.: 59417 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.874 AC: 133102 AN: 152234 Hom.: 59445 Cov.: 32 AF XY: 0.867 AC XY: 64539 AN XY: 74432

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.868

Alfa AF: 0.929 Hom.: 126247

Bravo AF: 0.865

Asia WGS AF: 0.550 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2905325; hg19: chr7-22712877;