7-22723798-C-T

Position:

• chr7-22723798-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 0.0556 in 152,268 control chromosomes in the GnomAD database, including 557 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 0.056 (557 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22723798C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+3770G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8449 AN: 152150 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0556 AC: 8467 AN: 152268 Hom.: 557 Cov.: 32 AF XY: 0.0550 AC XY: 4095 AN XY: 74442

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0527 Hom.: 76

Bravo AF: 0.0625

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
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: rs3087221; hg19: chr7-22763417;