rs543293

Variant names:

• chr11-86109035-A-G
• rs543293

Your query was ambiguous. Multiple possible variants found:

• chr11-86109035-A-G
• chr11-86109035-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 0.719 in 152,108 control chromosomes in the GnomAD database, including 39,910 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 0.72 (39910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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: 0.719 AC: 109218 AN: 151990 Hom.: 39868 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.719 AC: 109316 AN: 152108 Hom.: 39910 Cov.: 32 AF XY: 0.715 AC XY: 53178 AN XY: 74356

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.718

Alfa AF: 0.677 Hom.: 47547

Bravo AF: 0.725

Asia WGS AF: 0.616 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs543293; hg19: chr11-85820077;