rs11918665

Variant names:

• chr3-186495995-A-G
• rs11918665

Your query was ambiguous. Multiple possible variants found:

• chr3-186495995-A-G
• chr3-186495995-A-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 0.904 in 152,330 control chromosomes in the GnomAD database, including 62,374 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 0.90 (62374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.965 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: 0.904 AC: 137533 AN: 152212 Hom.: 62317 Cov.: 33

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.904 AC: 137649 AN: 152330 Hom.: 62374 Cov.: 33 AF XY: 0.905 AC XY: 67383 AN XY: 74470

African (AFR) AF: 0.973 AC: 40444 AN: 41586

American (AMR) AF: 0.898 AC: 13742 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.946 AC: 4910 AN: 5188

South Asian (SAS) AF: 0.863 AC: 4165 AN: 4828

European-Finnish (FIN) AF: 0.884 AC: 9372 AN: 10604

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58997 AN: 68036

Other (OTH) AF: 0.895 AC: 1894 AN: 2116

Alfa AF: 0.879 Hom.: 95629

Bravo AF: 0.910

Asia WGS AF: 0.920 AC: 3201 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	3.5
DANN	Benign	0.70
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11918665; hg19: chr3-186213784;