rs1404008

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+11187A>T		intron_variant, non_coding_transcript_variant

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;