11-3849569-A-G

Variant names:

• chr11-3849569-A-G
• rs2193

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 0.838 in 152,190 control chromosomes in the GnomAD database, including 54,061 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 0.84 (54061 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 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: 0.838 AC: 127399 AN: 152072 Hom.: 54041 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.838 AC: 127473 AN: 152190 Hom.: 54061 Cov.: 33 AF XY: 0.831 AC XY: 61783 AN XY: 74390

African (AFR) AF: 0.724 AC: 30036 AN: 41488

American (AMR) AF: 0.787 AC: 12029 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3842 AN: 5186

South Asian (SAS) AF: 0.790 AC: 3815 AN: 4830

European-Finnish (FIN) AF: 0.848 AC: 8971 AN: 10584

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62925 AN: 68028

Other (OTH) AF: 0.841 AC: 1777 AN: 2114

Alfa AF: 0.887 Hom.: 119114

Bravo AF: 0.827

Asia WGS AF: 0.754 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2193; hg19: chr11-3870799;