rs2056576

chr7-22721583-C-T

Variant summary

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

The ENST00000650428.1(STEAP1B):n.46+5985G>A 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 0.336 in 151,842 control chromosomes in the GnomAD database, including 8,860 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 0.34 (8860 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

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 (AFR) allele frequency at 95% confidence interval = 0.4 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+5985G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50908 AN: 151726 Hom.: 8851 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.336 AC: 50955 AN: 151842 Hom.: 8860 Cov.: 32 AF XY: 0.331 AC XY: 24552 AN XY: 74220

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.339

Alfa AF: 0.333 Hom.: 11645

Bravo AF: 0.348

Asia WGS AF: 0.159 AC: 550 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	5.9
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056576; hg19: chr7-22761202;