rs10513401

Variant names:

• chr9-122358070-A-G
• rs10513401

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 0.21 in 152,056 control chromosomes in the GnomAD database, including 4,248 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 0.21 (4248 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.909

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.210 AC: 31876 AN: 151938 Hom.: 4249 Cov.: 31

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.210 AC: 31873 AN: 152056 Hom.: 4248 Cov.: 31 AF XY: 0.211 AC XY: 15647 AN XY: 74318

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0488

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.216

Alfa AF: 0.264 Hom.: 3078

Bravo AF: 0.197

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513401; hg19: chr9-125120349;