chr11-131039392-A-G

Variant names:

• chr11-131039392-A-G
• rs1793220

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 0.878 in 152,232 control chromosomes in the GnomAD database, including 58,976 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 0.88 (58976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

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 = 0.976 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: 0.878 AC: 133549 AN: 152114 Hom.: 58915 Cov.: 32

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.878 AC: 133668 AN: 152232 Hom.: 58976 Cov.: 32 AF XY: 0.881 AC XY: 65604 AN XY: 74432

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.859

Alfa AF: 0.859 Hom.: 9144

Bravo AF: 0.884

Asia WGS AF: 0.939 AC: 3265 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	0.029
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1793220; hg19: chr11-130909287;