rs543293

chr11-86109035-A-Gchr11-86109035-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;