chr15-48393978-A-G

Variant names:

• chr15-48393978-A-G
• rs10519170

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 0.18 in 151,770 control chromosomes in the GnomAD database, including 3,424 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 0.18 (3424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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 (EAS) allele frequency at 95% confidence interval = 0.529 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: 0.180 AC: 27261 AN: 151652 Hom.: 3406 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.180 AC: 27337 AN: 151770 Hom.: 3424 Cov.: 32 AF XY: 0.184 AC XY: 13658 AN XY: 74142

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.167

Alfa AF: 0.113 Hom.: 1176

Bravo AF: 0.184

Asia WGS AF: 0.424 AC: 1474 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	0.21
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519170; hg19: chr15-48686175;