rs266108

Variant names:

• chr10-44356672-G-A
• rs266108

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 0.0518 in 152,210 control chromosomes in the GnomAD database, including 234 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 0.052 (234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0696 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: 0.0518 AC: 7885 AN: 152092 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0518 AC: 7889 AN: 152210 Hom.: 234 Cov.: 32 AF XY: 0.0515 AC XY: 3830 AN XY: 74428

African (AFR) AF: 0.0353 AC: 1467 AN: 41538

American (AMR) AF: 0.0397 AC: 608 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 307 AN: 3462

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0761 AC: 366 AN: 4812

European-Finnish (FIN) AF: 0.0592 AC: 629 AN: 10620

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4319 AN: 67986

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0466 Hom.: 100

Bravo AF: 0.0466

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.79
PhyloP100		-0.96
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: rs266108; hg19: chr10-44852120;