rs9298628

Variant names:

• chr8-42750848-C-T
• rs9298628

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 0.355 in 151,768 control chromosomes in the GnomAD database, including 13,778 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 0.36 (13778 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.355 AC: 53821 AN: 151650 Hom.: 13729 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.355 AC: 53930 AN: 151768 Hom.: 13778 Cov.: 33 AF XY: 0.349 AC XY: 25884 AN XY: 74152

African (AFR) AF: 0.728 AC: 30178 AN: 41468

American (AMR) AF: 0.273 AC: 4167 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5160

South Asian (SAS) AF: 0.207 AC: 985 AN: 4752

European-Finnish (FIN) AF: 0.186 AC: 1959 AN: 10536

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13927 AN: 67830

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.243 Hom.: 3133

Bravo AF: 0.379

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9298628; hg19: chr8-42605991;