rs7033100

Variant names:

• chr9-80242979-G-A
• rs7033100

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 0.273 in 152,034 control chromosomes in the GnomAD database, including 6,551 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 0.27 (6551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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 (NFE) allele frequency at 95% confidence interval = 0.348 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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41465 AN: 151916 Hom.: 6554 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.273 AC: 41458 AN: 152034 Hom.: 6551 Cov.: 32 AF XY: 0.270 AC XY: 20058 AN XY: 74334

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.310

Alfa AF: 0.342 Hom.: 15511

Bravo AF: 0.261

Asia WGS AF: 0.178 AC: 622 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	0.24
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7033100; hg19: chr9-82857894;