chr11-4093309-G-A

Position:

• chr11-4093309-G-A

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 0.81 in 152,144 control chromosomes in the GnomAD database, including 51,871 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 0.81 (51871 hom., cov: 32)
  • Exomes 𝑓: 0.94 (150 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.810 AC: 123117 AN: 152026 Hom.: 51851 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.839

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.936 AC: 322 AN: 344 Hom.: 150 AF XY: 0.951 AC XY: 196 AN XY: 206

Gnomad4 FIN exome AF: 0.935

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.810 AC: 123177 AN: 152144 Hom.: 51871 Cov.: 32 AF XY: 0.813 AC XY: 60509 AN XY: 74388

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.838

Alfa AF: 0.893 Hom.: 65511

Bravo AF: 0.793

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1465952; hg19: chr11-4114539;