rs10519445

Variant names:

• chr15-23861661-G-A
• rs10519445

Your query was ambiguous. Multiple possible variants found:

• chr15-23861661-G-A
• chr15-23861661-G-C

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 0.432 in 151,990 control chromosomes in the GnomAD database, including 15,902 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 0.43 (15902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 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: 0.432 AC: 65600 AN: 151872 Hom.: 15895 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.432 AC: 65625 AN: 151990 Hom.: 15902 Cov.: 32 AF XY: 0.436 AC XY: 32386 AN XY: 74286

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.460

Alfa AF: 0.511 Hom.: 39199

Bravo AF: 0.420

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519445; hg19: chr15-24106808;