rs686803

Variant names:

• chr9-32579855-G-C
• rs686803

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 0.201 in 152,096 control chromosomes in the GnomAD database, including 3,490 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 0.20 (3490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30551 AN: 151978 Hom.: 3475 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.201 AC: 30594 AN: 152096 Hom.: 3490 Cov.: 32 AF XY: 0.198 AC XY: 14740 AN XY: 74366

African (AFR) AF: 0.319 AC: 13203 AN: 41448

American (AMR) AF: 0.145 AC: 2218 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5172

South Asian (SAS) AF: 0.123 AC: 596 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1499 AN: 10588

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10431 AN: 67998

Other (OTH) AF: 0.190 AC: 401 AN: 2108

Alfa AF: 0.182 Hom.: 338

Bravo AF: 0.207

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.32
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs686803; hg19: chr9-32579853;