rs826474

Variant names:

• chr10-2366658-A-G
• rs826474

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 0.704 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• 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

African (AFR) AF: 0.838 AC: 34807 AN: 41524

American (AMR) AF: 0.710 AC: 10854 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2042 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4288 AN: 5186

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4822

European-Finnish (FIN) AF: 0.706 AC: 7465 AN: 10576

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42542 AN: 67994

Other (OTH) AF: 0.671 AC: 1419 AN: 2116

Alfa AF: 0.651 Hom.: 128157

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs826474; hg19: chr10-2408852;