11-68649439-C-G

Variant names:

• chr11-68649439-C-G
• rs2513280

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 0.85 in 152,206 control chromosomes in the GnomAD database, including 55,122 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 (55122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129291 AN: 152088 Hom.: 55076 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.850 AC: 129391 AN: 152206 Hom.: 55122 Cov.: 33 AF XY: 0.854 AC XY: 63549 AN XY: 74418

African (AFR) AF: 0.817 AC: 33916 AN: 41520

American (AMR) AF: 0.837 AC: 12792 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3171 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4399 AN: 5176

South Asian (SAS) AF: 0.901 AC: 4345 AN: 4824

European-Finnish (FIN) AF: 0.909 AC: 9637 AN: 10600

Middle Eastern (MID) AF: 0.908 AC: 265 AN: 292

European-Non Finnish (NFE) AF: 0.859 AC: 58421 AN: 68016

Other (OTH) AF: 0.850 AC: 1797 AN: 2114

Alfa AF: 0.863 Hom.: 6624

Bravo AF: 0.838

Asia WGS AF: 0.890 AC: 3097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	17
DANN	Benign	0.45
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs2513280; hg19: chr11-68416907;