chr11-128870788-C-G

Variant names:

• chr11-128870788-C-G
• rs881333

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 0.709 in 152,070 control chromosomes in the GnomAD database, including 38,430 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 0.71 (38430 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• 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 = 0.806 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107796 AN: 151952 Hom.: 38389 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.709 AC: 107882 AN: 152070 Hom.: 38430 Cov.: 31 AF XY: 0.714 AC XY: 53064 AN XY: 74338

African (AFR) AF: 0.668 AC: 27735 AN: 41492

American (AMR) AF: 0.776 AC: 11862 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2500 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4259 AN: 5152

South Asian (SAS) AF: 0.634 AC: 3054 AN: 4820

European-Finnish (FIN) AF: 0.742 AC: 7850 AN: 10580

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48201 AN: 67962

Other (OTH) AF: 0.708 AC: 1489 AN: 2102

Alfa AF: 0.668 Hom.: 2274

Bravo AF: 0.709

Asia WGS AF: 0.742 AC: 2581 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	1.7
DANN	Benign	0.46
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs881333; hg19: chr11-128740683;