rs6952003

chr7-22713086-T-Achr7-22713086-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650428.1(STEAP1B):n.46+14482A>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+14482A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.261

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6952003; hg19: chr7-22752705;