rs11825709

Variant names:

• chr11-93970883-A-G
• rs11825709

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 0.0462 in 152,298 control chromosomes in the GnomAD database, including 310 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 0.046 (310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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: 0.0461 AC: 7018 AN: 152182 Hom.: 311 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0462 AC: 7030 AN: 152298 Hom.: 310 Cov.: 32 AF XY: 0.0479 AC XY: 3566 AN XY: 74478

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0311 Hom.: 43

Bravo AF: 0.0464

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11825709; hg19: chr11-93704049;