rs28699225

Variant names:

• chr19-9075711-G-A
• rs28699225

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 0.217 in 151,672 control chromosomes in the GnomAD database, including 3,631 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 0.22 (3631 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 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: 0.217 AC: 32911 AN: 151556 Hom.: 3628 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.217 AC: 32927 AN: 151672 Hom.: 3631 Cov.: 30 AF XY: 0.217 AC XY: 16107 AN XY: 74090

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.224

Alfa AF: 0.221 Hom.: 930

Bravo AF: 0.216

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28699225; hg19: chr19-9186387;