7-22502364-T-C

Variant names:

• chr7-22502364-T-C
• rs3857716
• ENST00000439708.1:c.-31-7478A>G

Variant summary

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

The ENST00000439708.1(STEAP1B):​c.-31-7478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,096 control chromosomes in the GnomAD database, including 6,604 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 0.29 (6604 hom., cov: 32)
• Consequence: STEAP1B ENST00000439708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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	ENST00000439708.1	c.-31-7478A>G		intron_variant	Intron 1 of 3	3		ENSP00000408954.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44265 AN: 151978 Hom.: 6614 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.291 AC: 44261 AN: 152096 Hom.: 6604 Cov.: 32 AF XY: 0.294 AC XY: 21871 AN XY: 74336

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.318

Alfa AF: 0.213 Hom.: 783

Bravo AF: 0.287

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3857716; hg19: chr7-22541983; COSMIC: COSV68346867;