rs10519040

Variant names:

• chr15-45951939-T-C
• rs10519040

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 0.325 in 152,058 control chromosomes in the GnomAD database, including 9,903 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 0.33 (9903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.325 AC: 49355 AN: 151940 Hom.: 9871 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.325 AC: 49437 AN: 152058 Hom.: 9903 Cov.: 33 AF XY: 0.320 AC XY: 23773 AN XY: 74342

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.275

Alfa AF: 0.309 Hom.: 1054

Bravo AF: 0.329

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519040; hg19: chr15-46244137;