rs2073990

chr7-22690342-G-A

Variant summary

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

The ENST00000650428.1(STEAP1B):n.46+37226C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,202 control chromosomes in the GnomAD database, including 56,141 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 0.85 (56141 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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 (NFE) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+37226C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128962 AN: 152084 Hom.: 56131 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.848 AC: 129013 AN: 152202 Hom.: 56141 Cov.: 33 AF XY: 0.842 AC XY: 62638 AN XY: 74416

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.948

Gnomad4 OTH AF: 0.851

Alfa AF: 0.877 Hom.: 8414

Bravo AF: 0.835

Asia WGS AF: 0.544 AC: 1895 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	0.30
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073990; hg19: chr7-22729961;