chr7-22710601-G-A

Variant names:

• chr7-22710601-G-A
• rs6954897
• ENST00000650428.1:n.46+16967C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+16967C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,176 control chromosomes in the GnomAD database, including 26,718 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 0.57 (26718 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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+16967C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86991 AN: 152058 Hom.: 26659 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.572 AC: 87113 AN: 152176 Hom.: 26718 Cov.: 33 AF XY: 0.580 AC XY: 43159 AN XY: 74368

African (AFR) AF: 0.730 AC: 30333 AN: 41530

American (AMR) AF: 0.648 AC: 9918 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3470

East Asian (EAS) AF: 0.964 AC: 5001 AN: 5186

South Asian (SAS) AF: 0.700 AC: 3386 AN: 4834

European-Finnish (FIN) AF: 0.446 AC: 4708 AN: 10552

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29935 AN: 67986

Other (OTH) AF: 0.612 AC: 1293 AN: 2112

Alfa AF: 0.491 Hom.: 17024

Bravo AF: 0.594

Asia WGS AF: 0.818 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.34
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6954897; hg19: chr7-22750220;