rs10894239

Variant names:

• chr11-130759227-C-A
• rs10894239

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 0.393 in 152,138 control chromosomes in the GnomAD database, including 11,929 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 (11929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 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: 0.393 AC: 59684 AN: 152020 Hom.: 11925 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.393 AC: 59735 AN: 152138 Hom.: 11929 Cov.: 32 AF XY: 0.394 AC XY: 29294 AN XY: 74370

African (AFR) AF: 0.337 AC: 13967 AN: 41494

American (AMR) AF: 0.452 AC: 6906 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1636 AN: 5184

South Asian (SAS) AF: 0.328 AC: 1577 AN: 4812

European-Finnish (FIN) AF: 0.444 AC: 4696 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27958 AN: 67990

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.403 Hom.: 23749

Bravo AF: 0.397

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.64
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs10894239; hg19: chr11-130629122;