rs2067074

Positions:

• chr7-22681324-G-C

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+46244C>G 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 0.558 in 152,104 control chromosomes in the GnomAD database, including 25,701 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 0.56 (25701 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+46244C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84886 AN: 151986 Hom.: 25704 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.558 AC: 84904 AN: 152104 Hom.: 25701 Cov.: 32 AF XY: 0.552 AC XY: 41014 AN XY: 74366

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.573

Alfa AF: 0.626 Hom.: 3871

Bravo AF: 0.537

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2067074; hg19: chr7-22720943;