chr9-99275688-A-G

Variant names:

• chr9-99275688-A-G
• rs10819643

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 0.162 in 151,972 control chromosomes in the GnomAD database, including 2,438 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 0.16 (2438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24578 AN: 151854 Hom.: 2438 Cov.: 32

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.162 AC: 24579 AN: 151972 Hom.: 2438 Cov.: 32 AF XY: 0.166 AC XY: 12331 AN XY: 74262

African (AFR) AF: 0.0512 AC: 2124 AN: 41470

American (AMR) AF: 0.169 AC: 2583 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3466

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5158

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4810

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10544

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13726 AN: 67946

Other (OTH) AF: 0.152 AC: 321 AN: 2106

Alfa AF: 0.188 Hom.: 2054

Bravo AF: 0.150

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs10819643; hg19: chr9-102037970;