rs266109

Variant names:

• chr10-44354976-G-A
• rs266109

Your query was ambiguous. Multiple possible variants found:

• chr10-44354976-G-A
• chr10-44354976-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.848 in 152,248 control chromosomes in the GnomAD database, including 55,197 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 0.85 (55197 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.848 AC: 129041 AN: 152130 Hom.: 55159 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.848 AC: 129129 AN: 152248 Hom.: 55197 Cov.: 33 AF XY: 0.851 AC XY: 63353 AN XY: 74436

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.860

Alfa AF: 0.880 Hom.: 57832

Bravo AF: 0.830

Asia WGS AF: 0.930 AC: 3233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.059
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266109; hg19: chr10-44850424;