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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.738 AC: 30627 AN: 41510

American (AMR) AF: 0.811 AC: 12399 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2964 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5054 AN: 5184

South Asian (SAS) AF: 0.944 AC: 4553 AN: 4824

European-Finnish (FIN) AF: 0.939 AC: 9972 AN: 10616

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60648 AN: 68028

Other (OTH) AF: 0.860 AC: 1819 AN: 2114

Alfa AF: 0.873 Hom.: 73577

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
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs266109; hg19: chr10-44850424;