11-58768358-A-G

Variant names:

• chr11-58768358-A-G
• rs1938709

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.452 AC: 18707 AN: 41414

American (AMR) AF: 0.675 AC: 10306 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2969 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2523 AN: 5144

South Asian (SAS) AF: 0.627 AC: 3021 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7136 AN: 10582

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54892 AN: 67980

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.763 Hom.: 23736

Bravo AF: 0.663

Asia WGS AF: 0.527 AC: 1833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1938709; hg19: chr11-58535831;