rs11914380

Variant names:

• chr3-86846858-C-T
• rs11914380

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 0.0586 in 150,588 control chromosomes in the GnomAD database, including 605 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 0.059 (605 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.0585 AC: 8802 AN: 150484 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0226

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.00612

Gnomad OTH AF: 0.0681

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

GnomAD4 genome AF: 0.0586 AC: 8829 AN: 150588 Hom.: 605 Cov.: 31 AF XY: 0.0611 AC XY: 4490 AN XY: 73490

African (AFR) AF: 0.109 AC: 4451 AN: 40828

American (AMR) AF: 0.165 AC: 2489 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.0226 AC: 78 AN: 3456

East Asian (EAS) AF: 0.186 AC: 934 AN: 5034

South Asian (SAS) AF: 0.0103 AC: 49 AN: 4740

European-Finnish (FIN) AF: 0.0254 AC: 262 AN: 10330

Middle Eastern (MID) AF: 0.00694 AC: 2 AN: 288

European-Non Finnish (NFE) AF: 0.00612 AC: 415 AN: 67834

Other (OTH) AF: 0.0713 AC: 149 AN: 2090

Alfa AF: 0.0267 Hom.: 953

Bravo AF: 0.0752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs11914380; hg19: chr3-86896008;