rs2106549

Positions:

• chr7-22693350-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+34218C>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 0.886 in 151,938 control chromosomes in the GnomAD database, including 60,839 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 0.89 (60839 hom., cov: 28)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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+34218C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134515 AN: 151822 Hom.: 60802 Cov.: 28

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.886 AC: 134605 AN: 151938 Hom.: 60839 Cov.: 28 AF XY: 0.879 AC XY: 65261 AN XY: 74282

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.873

Alfa AF: 0.921 Hom.: 26497

Bravo AF: 0.878

Asia WGS AF: 0.557 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2106549; hg19: chr7-22732969;