11-26061823-T-A

Variant names:

• chr11-26061823-T-A
• rs1994547

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 0.826 in 152,022 control chromosomes in the GnomAD database, including 52,760 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 0.83 (52760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.826 AC: 125474 AN: 151904 Hom.: 52754 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.826 AC: 125515 AN: 152022 Hom.: 52760 Cov.: 32 AF XY: 0.830 AC XY: 61717 AN XY: 74332

African (AFR) AF: 0.653 AC: 27072 AN: 41460

American (AMR) AF: 0.873 AC: 13297 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2954 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4981 AN: 5172

South Asian (SAS) AF: 0.902 AC: 4356 AN: 4828

European-Finnish (FIN) AF: 0.945 AC: 10023 AN: 10610

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60120 AN: 67940

Other (OTH) AF: 0.836 AC: 1764 AN: 2110

Alfa AF: 0.859 Hom.: 7026

Bravo AF: 0.812

Asia WGS AF: 0.906 AC: 3148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.73
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1994547; hg19: chr11-26083370;