rs10813797

Variant names:

• chr9-32359193-C-A
• rs10813797

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 0.364 in 151,956 control chromosomes in the GnomAD database, including 10,763 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 0.36 (10763 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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: 0.364 AC: 55325 AN: 151840 Hom.: 10760 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.364 AC: 55341 AN: 151956 Hom.: 10763 Cov.: 32 AF XY: 0.362 AC XY: 26849 AN XY: 74260

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.377

Alfa AF: 0.417 Hom.: 6786

Bravo AF: 0.360

Asia WGS AF: 0.309 AC: 1070 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10813797; hg19: chr9-32359191;