chr7-22717884-C-T

Position:

• chr7-22717884-C-T

Variant summary

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

The variant allele was found at a frequency of 0.588 in 152,020 control chromosomes in the GnomAD database, including 27,858 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 (27858 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

Genes affected

(HGNC:):

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 = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22717884C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+9684G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89307 AN: 151902 Hom.: 27836 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.588 AC: 89390 AN: 152020 Hom.: 27858 Cov.: 32 AF XY: 0.583 AC XY: 43312 AN XY: 74296

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.603

Alfa AF: 0.563 Hom.: 4527

Bravo AF: 0.612

Asia WGS AF: 0.394 AC: 1368 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	4.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1546762; hg19: chr7-22757503;