rs10815798

Variant names:

• chr9-8235633-A-G
• rs10815798

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.457 in 152,056 control chromosomes in the GnomAD database, including 17,334 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 0.46 (17334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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: 0.457 AC: 69464 AN: 151938 Hom.: 17333 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.457 AC: 69478 AN: 152056 Hom.: 17334 Cov.: 32 AF XY: 0.463 AC XY: 34441 AN XY: 74314

African (AFR) AF: 0.250 AC: 10354 AN: 41474

American (AMR) AF: 0.529 AC: 8080 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2094 AN: 5164

South Asian (SAS) AF: 0.533 AC: 2568 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6355 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36830 AN: 67970

Other (OTH) AF: 0.471 AC: 995 AN: 2114

Alfa AF: 0.501 Hom.: 57048

Bravo AF: 0.441

Asia WGS AF: 0.447 AC: 1551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.67
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10815798; hg19: chr9-8235633;