11-94415267-C-G

Variant names:

• chr11-94415267-C-G
• rs491404

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 0.659 in 152,098 control chromosomes in the GnomAD database, including 33,218 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 0.66 (33218 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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: 0.659 AC: 100200 AN: 151980 Hom.: 33191 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.659 AC: 100280 AN: 152098 Hom.: 33218 Cov.: 33 AF XY: 0.663 AC XY: 49302 AN XY: 74366

African (AFR) AF: 0.637 AC: 26443 AN: 41480

American (AMR) AF: 0.672 AC: 10264 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3744 AN: 5170

South Asian (SAS) AF: 0.774 AC: 3731 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7087 AN: 10572

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44890 AN: 67992

Other (OTH) AF: 0.666 AC: 1402 AN: 2106

Alfa AF: 0.648 Hom.: 3971

Bravo AF: 0.655

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.40
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs491404; hg19: chr11-94148433;