11-117880025-C-G

Variant names:

• chr11-117880025-C-G
• rs497768

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 0.538 in 151,876 control chromosomes in the GnomAD database, including 22,282 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 0.54 (22282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81651 AN: 151758 Hom.: 22283 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.538 AC: 81679 AN: 151876 Hom.: 22282 Cov.: 31 AF XY: 0.532 AC XY: 39441 AN XY: 74196

African (AFR) AF: 0.449 AC: 18572 AN: 41390

American (AMR) AF: 0.574 AC: 8761 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2426 AN: 3466

East Asian (EAS) AF: 0.667 AC: 3442 AN: 5160

South Asian (SAS) AF: 0.596 AC: 2868 AN: 4810

European-Finnish (FIN) AF: 0.434 AC: 4570 AN: 10540

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39060 AN: 67928

Other (OTH) AF: 0.555 AC: 1168 AN: 2106

Alfa AF: 0.552 Hom.: 2932

Bravo AF: 0.539

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs497768; hg19: chr11-117750740;