11-2052683-A-G

Variant names:

• chr11-2052683-A-G
• rs7925515

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 0.798 in 151,414 control chromosomes in the GnomAD database, including 48,509 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 0.80 (48509 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849

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 (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.798 AC: 120690 AN: 151298 Hom.: 48450 Cov.: 28

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.798 AC: 120808 AN: 151414 Hom.: 48509 Cov.: 28 AF XY: 0.794 AC XY: 58676 AN XY: 73944

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.798

Alfa AF: 0.765 Hom.: 68027

Bravo AF: 0.811

Asia WGS AF: 0.676 AC: 2350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925515; hg19: chr11-2073913;