11-68659776-A-G

Variant names:

• chr11-68659776-A-G
• rs2156464

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 0.865 in 152,196 control chromosomes in the GnomAD database, including 57,129 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 0.87 (57129 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.865 AC: 131538 AN: 152078 Hom.: 57069 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.865 AC: 131656 AN: 152196 Hom.: 57129 Cov.: 31 AF XY: 0.869 AC XY: 64630 AN XY: 74404

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.853

Alfa AF: 0.841 Hom.: 24284

Bravo AF: 0.858

Asia WGS AF: 0.899 AC: 3124 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156464; hg19: chr11-68427244;