rs399208

Variant names:

• chr11-55660046-A-G
• rs399208

Your query was ambiguous. Multiple possible variants found:

• chr11-55660046-A-G
• chr11-55660046-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.533 in 135,402 control chromosomes in the GnomAD database, including 25,219 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 (25219 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.533 AC: 72098 AN: 135322 Hom.: 25211 Cov.: 23

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.489

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.533 AC: 72143 AN: 135402 Hom.: 25219 Cov.: 23 AF XY: 0.533 AC XY: 34876 AN XY: 65466

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.528

Alfa AF: 0.536 Hom.: 2167

Asia WGS AF: 0.680 AC: 2104 AN: 3092

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs399208; hg19: chr11-55427522;