rs10894115

Variant names:

• chr11-129695182-C-G
• rs10894115

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 0.402 in 152,182 control chromosomes in the GnomAD database, including 12,806 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 0.40 (12806 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61110 AN: 152064 Hom.: 12798 Cov.: 34

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.402 AC: 61156 AN: 152182 Hom.: 12806 Cov.: 34 AF XY: 0.397 AC XY: 29517 AN XY: 74412

African (AFR) AF: 0.328 AC: 13617 AN: 41536

American (AMR) AF: 0.341 AC: 5219 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1730 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1297 AN: 5168

South Asian (SAS) AF: 0.547 AC: 2642 AN: 4832

European-Finnish (FIN) AF: 0.377 AC: 3994 AN: 10598

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31282 AN: 67962

Other (OTH) AF: 0.445 AC: 942 AN: 2116

Alfa AF: 0.432 Hom.: 1775

Bravo AF: 0.392

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.65
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10894115; hg19: chr11-129565077;