11-94314460-C-T

Variant names:

• chr11-94314460-C-T
• rs493390

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 0.525 in 151,972 control chromosomes in the GnomAD database, including 22,818 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 0.53 (22818 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.526 AC: 79830 AN: 151854 Hom.: 22818 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.525 AC: 79845 AN: 151972 Hom.: 22818 Cov.: 31 AF XY: 0.527 AC XY: 39163 AN XY: 74270

African (AFR) AF: 0.283 AC: 11722 AN: 41414

American (AMR) AF: 0.582 AC: 8892 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3466

East Asian (EAS) AF: 0.631 AC: 3256 AN: 5160

South Asian (SAS) AF: 0.442 AC: 2125 AN: 4804

European-Finnish (FIN) AF: 0.655 AC: 6922 AN: 10568

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42511 AN: 67972

Other (OTH) AF: 0.573 AC: 1207 AN: 2108

Alfa AF: 0.591 Hom.: 94303

Bravo AF: 0.516

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs493390; hg19: chr11-94047626;