rs1404008

Variant names:

• chr7-22716381-T-A
• rs1404008
• ENST00000650428.1:n.46+11187A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22716381-T-A
• chr7-22716381-T-C

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+11187A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,144 control chromosomes in the GnomAD database, including 28,234 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 0.59 (28234 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+11187A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89833 AN: 152026 Hom.: 28211 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.591 AC: 89915 AN: 152144 Hom.: 28234 Cov.: 33 AF XY: 0.586 AC XY: 43567 AN XY: 74374

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.603

Alfa AF: 0.554 Hom.: 3044

Bravo AF: 0.615

Asia WGS AF: 0.394 AC: 1367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.30
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404008; hg19: chr7-22756000;