rs2961283

chr7-22600879-G-A

Variant summary

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

The ENST00000442252.1(STEAP1B):n.129-28119C>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 0.491 in 152,068 control chromosomes in the GnomAD database, including 20,141 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 (20141 hom., cov: 32)
• Consequence: STEAP1B ENST00000442252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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.129-28119C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000658234.1	n.221-81G>A		intron_variant, non_coding_transcript_variant
STEAP1B	ENST00000439708.1	c.-32+31931C>T		intron_variant		3
STEAP1B	ENST00000650428.1	n.160-28119C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74661 AN: 151950 Hom.: 20138 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.491 AC: 74683 AN: 152068 Hom.: 20141 Cov.: 32 AF XY: 0.482 AC XY: 35789 AN XY: 74320

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.482

Alfa AF: 0.573 Hom.: 12678

Bravo AF: 0.471

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2961283; hg19: chr7-22640498;