rs11045913

Variant names:

• chr12-21263479-A-G
• rs11045913

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 0.497 in 152,072 control chromosomes in the GnomAD database, including 20,528 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 0.50 (20528 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• 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 (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.498 AC: 75627 AN: 151954 Hom.: 20529 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.497 AC: 75634 AN: 152072 Hom.: 20528 Cov.: 33 AF XY: 0.508 AC XY: 37745 AN XY: 74326

African (AFR) AF: 0.268 AC: 11124 AN: 41486

American (AMR) AF: 0.608 AC: 9288 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3264 AN: 5160

South Asian (SAS) AF: 0.516 AC: 2484 AN: 4812

European-Finnish (FIN) AF: 0.679 AC: 7185 AN: 10586

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38707 AN: 67974

Other (OTH) AF: 0.520 AC: 1099 AN: 2114

Alfa AF: 0.551 Hom.: 44384

Bravo AF: 0.485

Asia WGS AF: 0.539 AC: 1873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11045913; hg19: chr12-21416413;