rs10813083

Variant names:

• chr9-29423653-A-G
• rs10813083

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 0.0428 in 151,518 control chromosomes in the GnomAD database, including 187 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 0.043 (187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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 (EAS) allele frequency at 95% confidence interval = 0.0829 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: 0.0427 AC: 6466 AN: 151400 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0252

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0380

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

GnomAD4 genome AF: 0.0428 AC: 6487 AN: 151518 Hom.: 187 Cov.: 32 AF XY: 0.0421 AC XY: 3118 AN XY: 74040

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0252

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0376

Alfa AF: 0.0378 Hom.: 15

Bravo AF: 0.0465

Asia WGS AF: 0.0520 AC: 179 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.021
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10813083; hg19: chr9-29423651; COSMIC: COSV69456987;