rs10155981

Positions:

• chr7-22716844-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+10724G>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 0.208 in 150,232 control chromosomes in the GnomAD database, including 4,981 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 0.21 (4981 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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 (AFR) allele frequency at 95% confidence interval = 0.436 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+10724G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31277 AN: 150158 Hom.: 4975 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00254

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.208 AC: 31318 AN: 150232 Hom.: 4981 Cov.: 31 AF XY: 0.209 AC XY: 15313 AN XY: 73160

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.00255

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.198

Alfa AF: 0.126 Hom.: 1364

Bravo AF: 0.220

Asia WGS AF: 0.0900 AC: 313 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	5.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10155981; hg19: chr7-22756463;