rs6969502

Variant names:

• chr7-22712807-G-A
• rs6969502
• ENST00000650428.1:n.46+14761C>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+14761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,024 control chromosomes in the GnomAD database, including 9,506 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 0.32 (9506 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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+14761C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49023 AN: 151906 Hom.: 9485 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.323 AC: 49088 AN: 152024 Hom.: 9506 Cov.: 32 AF XY: 0.330 AC XY: 24485 AN XY: 74300

African (AFR) AF: 0.505 AC: 20931 AN: 41436

American (AMR) AF: 0.322 AC: 4919 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3283 AN: 5174

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4818

European-Finnish (FIN) AF: 0.280 AC: 2961 AN: 10562

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12915 AN: 67974

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.242 Hom.: 21097

Bravo AF: 0.333

Asia WGS AF: 0.492 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.40
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6969502; hg19: chr7-22752426;