11-76577893-G-A

Variant names:

• chr11-76577893-G-A
• rs10899234

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 0.385 in 152,120 control chromosomes in the GnomAD database, including 12,151 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 0.39 (12151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.385 AC: 58523 AN: 152002 Hom.: 12133 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.385 AC: 58595 AN: 152120 Hom.: 12151 Cov.: 33 AF XY: 0.381 AC XY: 28349 AN XY: 74372

African (AFR) AF: 0.551 AC: 22853 AN: 41488

American (AMR) AF: 0.278 AC: 4259 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3470

East Asian (EAS) AF: 0.157 AC: 811 AN: 5180

South Asian (SAS) AF: 0.281 AC: 1353 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3890 AN: 10568

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23347 AN: 67982

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.349 Hom.: 18912

Bravo AF: 0.385

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10899234; hg19: chr11-76288937;