7-22723390-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 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+4178G>C		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0675

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.166

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12700386; hg19: chr7-22763009;