rs1880242

chr7-22719988-G-T

Variant summary

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

The ENST00000650428.1(STEAP1B):n.46+7580C>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 0.595 in 152,090 control chromosomes in the GnomAD database, including 28,727 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 0.60 (28727 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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+7580C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90419 AN: 151972 Hom.: 28696 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.595 AC: 90512 AN: 152090 Hom.: 28727 Cov.: 32 AF XY: 0.590 AC XY: 43843 AN XY: 74316

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.607

Alfa AF: 0.536 Hom.: 11444

Bravo AF: 0.620

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880242; hg19: chr7-22759607;