rs399208

chr11-55660046-A-Gchr11-55660046-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;