rs3087221

Variant names:

• chr7-22723798-C-T
• rs3087221
• ENST00000650428.1:n.46+3770G>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+3770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,268 control chromosomes in the GnomAD database, including 557 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 0.056 (557 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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+3770G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8449 AN: 152150 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0556 AC: 8467 AN: 152268 Hom.: 557 Cov.: 32 AF XY: 0.0550 AC XY: 4095 AN XY: 74442

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0527 Hom.: 76

Bravo AF: 0.0625

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087221; hg19: chr7-22763417;