7-22467075-G-A

Variant names:

• chr7-22467075-G-A
• rs2893079
• NM_001382447.1:c.762+25490C>T

Variant summary

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

The NM_001382447.1(STEAP1B):​c.762+25490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,256 control chromosomes in the GnomAD database, including 56,710 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 0.86 (56710 hom., cov: 32)
• Consequence: STEAP1B NM_001382447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 2 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=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP1B	NM_001382447.1	c.762+25490C>T		intron_variant	Intron 4 of 4	ENST00000678116.1	NP_001369376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000678116.1	c.762+25490C>T		intron_variant	Intron 4 of 4		NM_001382447.1	ENSP00000503251.1
STEAP1B	ENST00000404369.8	c.762+25490C>T		intron_variant	Intron 4 of 4	1		ENSP00000384370.4
STEAP1B	ENST00000406890.6	c.705+25490C>T		intron_variant	Intron 4 of 4	1		ENSP00000385239.2

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130648 AN: 152138 Hom.: 56634 Cov.: 32

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.859 AC: 130785 AN: 152256 Hom.: 56710 Cov.: 32 AF XY: 0.862 AC XY: 64207 AN XY: 74450

African (AFR) AF: 0.964 AC: 40034 AN: 41548

American (AMR) AF: 0.864 AC: 13212 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5186 AN: 5190

South Asian (SAS) AF: 0.947 AC: 4571 AN: 4828

European-Finnish (FIN) AF: 0.804 AC: 8530 AN: 10604

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

European-Non Finnish (NFE) AF: 0.787 AC: 53546 AN: 68008

Other (OTH) AF: 0.845 AC: 1786 AN: 2114

Alfa AF: 0.818 Hom.: 28127

Bravo AF: 0.866

Asia WGS AF: 0.971 AC: 3376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	8.0
DANN	Benign	0.43
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2893079; hg19: chr7-22506694;