rs2097677

Positions:

• chr7-22693220-G-A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+34348C>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 0.24 in 151,614 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 30)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+34348C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36309 AN: 151494 Hom.: 4442 Cov.: 30

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.240 AC: 36316 AN: 151614 Hom.: 4445 Cov.: 30 AF XY: 0.241 AC XY: 17821 AN XY: 74098

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.239

Alfa AF: 0.242 Hom.: 555

Bravo AF: 0.240

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097677; hg19: chr7-22732839;