rs2905308

chr7-22608575-G-A

Variant summary

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

The ENST00000442252.1(STEAP1B):n.129-35815C>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 0.488 in 152,026 control chromosomes in the GnomAD database, including 19,952 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 0.49 (19952 hom., cov: 32)
• Consequence: STEAP1B ENST00000442252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 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	ENST00000442252.1	n.129-35815C>T		intron_variant, non_coding_transcript_variant		1
STEAP1B	ENST00000439708.1	c.-32+24235C>T		intron_variant		3
STEAP1B	ENST00000650428.1	n.159+24235C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74090 AN: 151908 Hom.: 19948 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74115 AN: 152026 Hom.: 19952 Cov.: 32 AF XY: 0.478 AC XY: 35535 AN XY: 74316

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.0518

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.480

Alfa AF: 0.570 Hom.: 12189

Bravo AF: 0.467

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.46
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2905308; hg19: chr7-22648194;