11-68647767-G-T

Variant names:

• chr11-68647767-G-T
• rs4930588

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 0.848 in 152,140 control chromosomes in the GnomAD database, including 54,861 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 0.85 (54861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.878 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: 0.848 AC: 128959 AN: 152022 Hom.: 54817 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.848 AC: 129057 AN: 152140 Hom.: 54861 Cov.: 32 AF XY: 0.852 AC XY: 63403 AN XY: 74388

African (AFR) AF: 0.810 AC: 33616 AN: 41478

American (AMR) AF: 0.837 AC: 12787 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3167 AN: 3468

East Asian (EAS) AF: 0.849 AC: 4382 AN: 5162

South Asian (SAS) AF: 0.901 AC: 4349 AN: 4828

European-Finnish (FIN) AF: 0.909 AC: 9638 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58415 AN: 68006

Other (OTH) AF: 0.848 AC: 1790 AN: 2110

Alfa AF: 0.855 Hom.: 9076

Bravo AF: 0.836

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs4930588; hg19: chr11-68415235;