11-129697815-A-G

Position:

• chr11-129697815-A-G

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 0.784 in 152,028 control chromosomes in the GnomAD database, including 50,450 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 0.78 (50450 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129697815A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119199 AN: 151910 Hom.: 50447 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.784 AC: 119245 AN: 152028 Hom.: 50450 Cov.: 32 AF XY: 0.789 AC XY: 58660 AN XY: 74302

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.824

Alfa AF: 0.901 Hom.: 64930

Bravo AF: 0.758

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10894116; hg19: chr11-129567710;