7-22715149-G-T

Variant names:

• chr7-22715149-G-T
• rs7776857
• ENST00000650428.1:n.46+12419C>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+12419C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,124 control chromosomes in the GnomAD database, including 47,241 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 0.78 (47241 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 14 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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+12419C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118026 AN: 152004 Hom.: 47169 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.777 AC: 118159 AN: 152124 Hom.: 47241 Cov.: 31 AF XY: 0.780 AC XY: 57985 AN XY: 74378

African (AFR) AF: 0.940 AC: 39033 AN: 41504

American (AMR) AF: 0.836 AC: 12794 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2728 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5180

South Asian (SAS) AF: 0.858 AC: 4136 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6483 AN: 10574

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45232 AN: 67956

Other (OTH) AF: 0.805 AC: 1704 AN: 2116

Alfa AF: 0.720 Hom.: 40997

Bravo AF: 0.802

Asia WGS AF: 0.930 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.41
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7776857; hg19: chr7-22754768;