rs10490947

Variant names:

• chr10-9106732-C-T
• rs10490947

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 0.0266 in 152,036 control chromosomes in the GnomAD database, including 139 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 0.027 (139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.996

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.098 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: 0.0265 AC: 4032 AN: 151918 Hom.: 134 Cov.: 31

Gnomad AFR AF: 0.00600

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0266 AC: 4050 AN: 152036 Hom.: 139 Cov.: 31 AF XY: 0.0284 AC XY: 2112 AN XY: 74292

Gnomad4 AFR AF: 0.00598

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0263 Hom.: 12

Bravo AF: 0.0316

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490947; hg19: chr10-9148695;