rs12808199

Variant names:

• chr11-39306409-G-A
• rs12808199

Your query was ambiguous. Multiple possible variants found:

• chr11-39306409-G-A
• chr11-39306409-G-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 0.478 in 151,924 control chromosomes in the GnomAD database, including 20,552 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 0.48 (20552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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: 0.478 AC: 72565 AN: 151806 Hom.: 20547 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.478 AC: 72583 AN: 151924 Hom.: 20552 Cov.: 32 AF XY: 0.482 AC XY: 35773 AN XY: 74240

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.517

Alfa AF: 0.590 Hom.: 38167

Bravo AF: 0.457

Asia WGS AF: 0.457 AC: 1589 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12808199; hg19: chr11-39327959;