rs10520789

Variant names:

• chr15-95598638-G-A
• rs10520789

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.115 in 152,286 control chromosomes in the GnomAD database, including 1,148 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 0.12 (1148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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: 0.115 AC: 17559 AN: 152168 Hom.: 1149 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.115 AC: 17561 AN: 152286 Hom.: 1148 Cov.: 33 AF XY: 0.109 AC XY: 8086 AN XY: 74454

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0582

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.105

Alfa AF: 0.113 Hom.: 1204

Bravo AF: 0.120

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	18
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: rs10520789; hg19: chr15-96141867;