rs10491833

Variant names:

• chr9-24720234-T-C
• rs10491833

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 0.177 in 151,508 control chromosomes in the GnomAD database, including 2,906 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 0.18 (2906 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.177 AC: 26801 AN: 151392 Hom.: 2901 Cov.: 31

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.177 AC: 26820 AN: 151508 Hom.: 2906 Cov.: 31 AF XY: 0.179 AC XY: 13207 AN XY: 73988

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.170

Alfa AF: 0.217 Hom.: 2067

Bravo AF: 0.167

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491833; hg19: chr9-24720232;