rs12808199

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;