11-1643386-C-A

Variant names:

• chr11-1643386-C-A
• rs902215

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 0.776 in 151,896 control chromosomes in the GnomAD database, including 45,880 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 0.78 (45880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.776 AC: 117815 AN: 151778 Hom.: 45852 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.776 AC: 117892 AN: 151896 Hom.: 45880 Cov.: 31 AF XY: 0.780 AC XY: 57913 AN XY: 74252

African (AFR) AF: 0.715 AC: 29630 AN: 41422

American (AMR) AF: 0.786 AC: 12016 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2628 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4482 AN: 5102

South Asian (SAS) AF: 0.800 AC: 3843 AN: 4806

European-Finnish (FIN) AF: 0.846 AC: 8955 AN: 10582

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53798 AN: 67922

Other (OTH) AF: 0.772 AC: 1629 AN: 2110

Alfa AF: 0.787 Hom.: 9510

Bravo AF: 0.769

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.4
DANN	Benign	0.89
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs902215; hg19: chr11-1664616;