11-68649439-C-G

Position:

• chr11-68649439-C-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 0.85 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.850

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2513280; hg19: chr11-68416907;