11-56026400-C-G

Variant names:

• chr11-56026400-C-G
• rs1384101

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 0.815 in 152,010 control chromosomes in the GnomAD database, including 50,757 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 0.81 (50757 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.815 AC: 123768 AN: 151892 Hom.: 50731 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.815 AC: 123839 AN: 152010 Hom.: 50757 Cov.: 31 AF XY: 0.817 AC XY: 60696 AN XY: 74290

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.826

Alfa AF: 0.750 Hom.: 2237

Bravo AF: 0.818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384101; hg19: chr11-55793876;