rs9300039

Variant names:

• chr11-41893816-C-A
• rs9300039

Your query was ambiguous. Multiple possible variants found:

• chr11-41893816-C-A
• chr11-41893816-C-T

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 0.1 in 151,638 control chromosomes in the GnomAD database, including 864 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 0.10 (864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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: 0.100 AC: 15147 AN: 151518 Hom.: 865 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.100 AC: 15166 AN: 151638 Hom.: 864 Cov.: 31 AF XY: 0.102 AC XY: 7545 AN XY: 74044

African (AFR) AF: 0.116 AC: 4798 AN: 41350

American (AMR) AF: 0.0706 AC: 1073 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1147 AN: 5122

South Asian (SAS) AF: 0.153 AC: 734 AN: 4794

European-Finnish (FIN) AF: 0.0823 AC: 864 AN: 10500

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0882 AC: 5990 AN: 67888

Other (OTH) AF: 0.0878 AC: 185 AN: 2106

Alfa AF: 0.0930 Hom.: 3143

Bravo AF: 0.100

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9300039; hg19: chr11-41915366;