ENST00000650428.1:n.46+9105C>T

Variant names:

• chr7-22718463-G-A
• rs7801617
• ENST00000650428.1:n.46+9105C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+9105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,118 control chromosomes in the GnomAD database, including 4,445 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 0.20 (4445 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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+9105C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30017 AN: 152000 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30052 AN: 152118 Hom.: 4445 Cov.: 32 AF XY: 0.198 AC XY: 14740 AN XY: 74370

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.191

Alfa AF: 0.132 Hom.: 2554

Bravo AF: 0.209

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7801617; hg19: chr7-22758082;