ENST00000650428.1:n.46+16168A>T

Variant names:

• chr7-22711400-T-A
• rs4552807
• ENST00000650428.1:n.46+16168A>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+16168A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,052 control chromosomes in the GnomAD database, including 28,051 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 0.58 (28051 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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+16168A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88740 AN: 151934 Hom.: 27993 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.584 AC: 88862 AN: 152052 Hom.: 28051 Cov.: 32 AF XY: 0.592 AC XY: 43978 AN XY: 74316

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.620

Alfa AF: 0.516 Hom.: 2687

Bravo AF: 0.609

Asia WGS AF: 0.833 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4552807; hg19: chr7-22751019;