11-131039392-A-G

Variant names:

• chr11-131039392-A-G
• rs1793220

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.959 AC: 39865 AN: 41552

American (AMR) AF: 0.895 AC: 13685 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5184

South Asian (SAS) AF: 0.838 AC: 4033 AN: 4814

European-Finnish (FIN) AF: 0.883 AC: 9365 AN: 10604

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55957 AN: 67996

Other (OTH) AF: 0.859 AC: 1817 AN: 2116

Alfa AF: 0.862 Hom.: 9496

Bravo AF: 0.884

Asia WGS AF: 0.939 AC: 3265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.029
DANN	Benign	0.44
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1793220; hg19: chr11-130909287;