rs10520033

chr15-35866461-G-T

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 0.0662 in 152,048 control chromosomes in the GnomAD database, including 765 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 0.066 (765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10040 AN: 151930 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0662 AC: 10065 AN: 152048 Hom.: 765 Cov.: 32 AF XY: 0.0631 AC XY: 4690 AN XY: 74326

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0467

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.00445

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0502 Hom.: 105

Bravo AF: 0.0756

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	10
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520033; hg19: chr15-36158662;