11-68649626-A-G

Variant names:

• chr11-68649626-A-G
• rs2513281

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 0.86 in 152,234 control chromosomes in the GnomAD database, including 56,367 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 0.86 (56367 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.879 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: 0.860 AC: 130792 AN: 152116 Hom.: 56312 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.860 AC: 130907 AN: 152234 Hom.: 56367 Cov.: 33 AF XY: 0.864 AC XY: 64277 AN XY: 74426

African (AFR) AF: 0.851 AC: 35328 AN: 41508

American (AMR) AF: 0.841 AC: 12876 AN: 15302

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

East Asian (EAS) AF: 0.849 AC: 4390 AN: 5172

South Asian (SAS) AF: 0.902 AC: 4349 AN: 4824

European-Finnish (FIN) AF: 0.909 AC: 9648 AN: 10612

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

European-Non Finnish (NFE) AF: 0.859 AC: 58422 AN: 68024

Other (OTH) AF: 0.856 AC: 1810 AN: 2114

Alfa AF: 0.858 Hom.: 136114

Bravo AF: 0.849

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.63
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2513281; hg19: chr11-68417094;