rs6952003

Variant names:

• chr7-22713086-T-A
• rs6952003
• ENST00000650428.1:n.46+14482A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22713086-T-A
• chr7-22713086-T-G

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+14482A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,122 control chromosomes in the GnomAD database, including 4,067 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 0.22 (4067 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 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+14482A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34110 AN: 152004 Hom.: 4061 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.224 AC: 34125 AN: 152122 Hom.: 4067 Cov.: 32 AF XY: 0.226 AC XY: 16796 AN XY: 74368

African (AFR) AF: 0.157 AC: 6517 AN: 41508

American (AMR) AF: 0.317 AC: 4840 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1353 AN: 5176

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1705 AN: 10576

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16763 AN: 67970

Other (OTH) AF: 0.261 AC: 550 AN: 2110

Alfa AF: 0.118 Hom.: 182

Bravo AF: 0.234

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6952003; hg19: chr7-22752705;