rs10491651

Variant names:

• chr9-5200060-A-G
• rs10491651

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 0.3 in 152,070 control chromosomes in the GnomAD database, including 6,973 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 0.30 (6973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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: 0.300 AC: 45626 AN: 151952 Hom.: 6965 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.300 AC: 45677 AN: 152070 Hom.: 6973 Cov.: 32 AF XY: 0.305 AC XY: 22644 AN XY: 74312

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.294

Alfa AF: 0.288 Hom.: 2959

Bravo AF: 0.292

Asia WGS AF: 0.313 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491651; hg19: chr9-5200060;