rs490726

Variant names:

• chr10-100368255-T-C
• rs490726

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 0.243 in 152,176 control chromosomes in the GnomAD database, including 5,413 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 0.24 (5413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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: 0.243 AC: 36925 AN: 152058 Hom.: 5377 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.243 AC: 37003 AN: 152176 Hom.: 5413 Cov.: 33 AF XY: 0.243 AC XY: 18108 AN XY: 74402

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.212

Alfa AF: 0.211 Hom.: 822

Bravo AF: 0.244

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490726; hg19: chr10-102128012;