15-49096052-G-A

Variant names:

• chr15-49096052-G-A
• rs10519208

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 0.247 in 151,996 control chromosomes in the GnomAD database, including 5,137 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 0.25 (5137 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37543 AN: 151878 Hom.: 5139 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.247 AC: 37556 AN: 151996 Hom.: 5137 Cov.: 31 AF XY: 0.250 AC XY: 18538 AN XY: 74298

African (AFR) AF: 0.201 AC: 8333 AN: 41480

American (AMR) AF: 0.376 AC: 5739 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2188 AN: 5146

South Asian (SAS) AF: 0.305 AC: 1467 AN: 4816

European-Finnish (FIN) AF: 0.184 AC: 1944 AN: 10556

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16144 AN: 67956

Other (OTH) AF: 0.287 AC: 605 AN: 2106

Alfa AF: 0.248 Hom.: 3595

Bravo AF: 0.261

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.44
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10519208; hg19: chr15-49388249;