chr11-127560939-A-G

Position:

• chr11-127560939-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 0.769 in 152,114 control chromosomes in the GnomAD database, including 45,656 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 0.77 (45656 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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 (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127560939A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116894 AN: 151996 Hom.: 45601 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.769 AC: 117010 AN: 152114 Hom.: 45656 Cov.: 32 AF XY: 0.770 AC XY: 57268 AN XY: 74348

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.752

Alfa AF: 0.701 Hom.: 7069

Bravo AF: 0.781

Asia WGS AF: 0.745 AC: 2589 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	0.032
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs356248; hg19: chr11-127430834;