11-114019986-A-G

Position:

• chr11-114019986-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 0.569 in 152,072 control chromosomes in the GnomAD database, including 24,873 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 0.57 (24873 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86449 AN: 151954 Hom.: 24877 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 152072 Hom.: 24873 Cov.: 33 AF XY: 0.567 AC XY: 42146 AN XY: 74318

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.550

Alfa AF: 0.593 Hom.: 3935

Bravo AF: 0.555

Asia WGS AF: 0.524 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2085421; hg19: chr11-113890708;