11-127596868-A-G

Position:

• chr11-127596868-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 0.619 in 152,100 control chromosomes in the GnomAD database, including 29,516 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 0.62 (29516 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127596868A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94096 AN: 151982 Hom.: 29496 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.619 AC: 94175 AN: 152100 Hom.: 29516 Cov.: 32 AF XY: 0.626 AC XY: 46505 AN XY: 74336

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.605

Alfa AF: 0.580 Hom.: 11715

Bravo AF: 0.621

Asia WGS AF: 0.648 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763300; hg19: chr11-127466763;