rs10813083

Positions:

• chr9-29423653-A-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.29423653A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;