rs826474

Variant names:

• chr10-2366658-A-G
• rs826474

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 0.704 in 152,180 control chromosomes in the GnomAD database, including 38,638 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 0.70 (38638 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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: 0.704 AC: 107077 AN: 152062 Hom.: 38586 Cov.: 34

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.704 AC: 107182 AN: 152180 Hom.: 38638 Cov.: 34 AF XY: 0.706 AC XY: 52545 AN XY: 74392

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.671

Alfa AF: 0.638 Hom.: 54327

Bravo AF: 0.713

Asia WGS AF: 0.736 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826474; hg19: chr10-2408852;