chr7-22718943-G-A

Position:

• chr7-22718943-G-A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+8625C>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 0.389 in 151,974 control chromosomes in the GnomAD database, including 11,593 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 0.39 (11593 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 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+8625C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58994 AN: 151856 Hom.: 11581 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.389 AC: 59047 AN: 151974 Hom.: 11593 Cov.: 32 AF XY: 0.383 AC XY: 28416 AN XY: 74272

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.409

Alfa AF: 0.401 Hom.: 16793

Bravo AF: 0.401

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7805828; hg19: chr7-22758562;