7-22723390-C-G

Variant names:

• chr7-22723390-C-G
• rs12700386
• ENST00000650428.1:n.46+4178G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650428.1(STEAP1B):​n.46+4178G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,236 control chromosomes in the GnomAD database, including 2,601 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 0.18 (2601 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• Publications: 38 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650428.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000650428.1		n.46+4178G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27554 AN: 152118 Hom.: 2590 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.181 AC: 27591 AN: 152236 Hom.: 2601 Cov.: 33 AF XY: 0.179 AC XY: 13326 AN XY: 74434

African (AFR) AF: 0.170 AC: 7069 AN: 41526

American (AMR) AF: 0.225 AC: 3450 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.0675 AC: 350 AN: 5184

South Asian (SAS) AF: 0.113 AC: 545 AN: 4832

European-Finnish (FIN) AF: 0.163 AC: 1724 AN: 10600

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13265 AN: 68004

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.0950 Hom.: 126

Bravo AF: 0.186

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.57
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs12700386; hg19: chr7-22763009;