rs7033100

Variant names:

• chr9-80242979-G-A
• rs7033100

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.153 AC: 6357 AN: 41476

American (AMR) AF: 0.234 AC: 3577 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3470

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5172

South Asian (SAS) AF: 0.344 AC: 1657 AN: 4820

European-Finnish (FIN) AF: 0.305 AC: 3223 AN: 10560

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23885 AN: 67950

Other (OTH) AF: 0.310 AC: 655 AN: 2116

Alfa AF: 0.325 Hom.: 33050

Bravo AF: 0.261

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.67
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7033100; hg19: chr9-82857894;