rs10519806

Variant names:

• chr15-33227852-C-G
• rs10519806

Your query was ambiguous. Multiple possible variants found:

• chr15-33227852-C-G
• chr15-33227852-C-T

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 0.369 in 152,020 control chromosomes in the GnomAD database, including 11,374 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 0.37 (11374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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: 0.369 AC: 56056 AN: 151902 Hom.: 11356 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.369 AC: 56104 AN: 152020 Hom.: 11374 Cov.: 32 AF XY: 0.360 AC XY: 26769 AN XY: 74318

African (AFR) AF: 0.503 AC: 20843 AN: 41454

American (AMR) AF: 0.303 AC: 4631 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5172

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23497 AN: 67954

Other (OTH) AF: 0.350 AC: 737 AN: 2106

Alfa AF: 0.351 Hom.: 1192

Bravo AF: 0.371

Asia WGS AF: 0.129 AC: 452 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10519806; hg19: chr15-33520053;