11-58768358-A-G

Position:

• chr11-58768358-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 0.672 in 152,002 control chromosomes in the GnomAD database, including 36,219 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 0.67 (36219 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

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 (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58768358A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102094 AN: 151884 Hom.: 36206 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.672 AC: 102139 AN: 152002 Hom.: 36219 Cov.: 31 AF XY: 0.666 AC XY: 49514 AN XY: 74310

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.737

Alfa AF: 0.760 Hom.: 21325

Bravo AF: 0.663

Asia WGS AF: 0.527 AC: 1833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938709; hg19: chr11-58535831;