rs10817049

Variant names:

• chr9-110609401-A-C
• rs10817049

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 0.159 in 152,180 control chromosomes in the GnomAD database, including 2,012 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 0.16 (2012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.159 AC: 24162 AN: 152062 Hom.: 2010 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.159 AC: 24182 AN: 152180 Hom.: 2012 Cov.: 33 AF XY: 0.158 AC XY: 11733 AN XY: 74384

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.161

Alfa AF: 0.165 Hom.: 387

Bravo AF: 0.155

Asia WGS AF: 0.0970 AC: 341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817049; hg19: chr9-113371681;