rs10813797

Positions:

• chr9-32359193-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;