rs10518784

Variant names:

• chr15-54829321-G-T
• rs10518784

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 0.207 in 152,102 control chromosomes in the GnomAD database, including 3,470 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 0.21 (3470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 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: 0.207 AC: 31402 AN: 151984 Hom.: 3465 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31427 AN: 152102 Hom.: 3470 Cov.: 32 AF XY: 0.203 AC XY: 15117 AN XY: 74372

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.206

Alfa AF: 0.234 Hom.: 8618

Bravo AF: 0.202

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518784; hg19: chr15-55121519;