rs7784987

Variant names:

• chr7-22721869-G-A
• rs7784987
• ENST00000650428.1:n.46+5699C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+5699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 152,298 control chromosomes in the GnomAD database, including 439 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 0.055 (439 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 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+5699C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8381 AN: 152180 Hom.: 437 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0206

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0552 AC: 8400 AN: 152298 Hom.: 439 Cov.: 32 AF XY: 0.0548 AC XY: 4078 AN XY: 74472

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0532

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0206

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0529 Hom.: 68

Bravo AF: 0.0613

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7784987; hg19: chr7-22761488;