chr15-48393978-A-G

Variant names:

• chr15-48393978-A-G
• rs10519170

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 0.18 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.298 AC: 12342 AN: 41364

American (AMR) AF: 0.146 AC: 2225 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2806 AN: 5144

South Asian (SAS) AF: 0.275 AC: 1320 AN: 4792

European-Finnish (FIN) AF: 0.127 AC: 1334 AN: 10506

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0974 AC: 6616 AN: 67920

Other (OTH) AF: 0.167 AC: 350 AN: 2102

Alfa AF: 0.127 Hom.: 2349

Bravo AF: 0.184

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.21
DANN	Benign	0.46
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10519170; hg19: chr15-48686175;