11-126281352-C-G

Variant names:

• chr11-126281352-C-G
• rs1786697

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 0.208 in 152,152 control chromosomes in the GnomAD database, including 4,386 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 0.21 (4386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31690 AN: 152034 Hom.: 4385 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.208 AC: 31690 AN: 152152 Hom.: 4386 Cov.: 32 AF XY: 0.221 AC XY: 16417 AN XY: 74392

African (AFR) AF: 0.0834 AC: 3465 AN: 41542

American (AMR) AF: 0.327 AC: 4997 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3466

East Asian (EAS) AF: 0.639 AC: 3296 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1652 AN: 4828

European-Finnish (FIN) AF: 0.259 AC: 2742 AN: 10572

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14085 AN: 67988

Other (OTH) AF: 0.217 AC: 456 AN: 2106

Alfa AF: 0.121 Hom.: 237

Bravo AF: 0.212

Asia WGS AF: 0.449 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.073
DANN	Benign	0.62
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1786697; hg19: chr11-126151247;