rs17725099

Variant names:

• chr19-18371548-G-A
• rs17725099

Your query was ambiguous. Multiple possible variants found:

• chr19-18371548-G-A
• chr19-18371548-G-C
• chr19-18371548-G-T

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 0.243 in 151,832 control chromosomes in the GnomAD database, including 4,548 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 0.24 (4548 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.273 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: 0.243 AC: 36897 AN: 151714 Hom.: 4546 Cov.: 30

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.243 AC: 36909 AN: 151832 Hom.: 4548 Cov.: 30 AF XY: 0.241 AC XY: 17892 AN XY: 74206

African (AFR) AF: 0.230 AC: 9506 AN: 41376

American (AMR) AF: 0.194 AC: 2963 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1339 AN: 5146

South Asian (SAS) AF: 0.286 AC: 1373 AN: 4804

European-Finnish (FIN) AF: 0.244 AC: 2567 AN: 10542

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17539 AN: 67940

Other (OTH) AF: 0.238 AC: 502 AN: 2108

Alfa AF: 0.248 Hom.: 19016

Bravo AF: 0.237

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs17725099; hg19: chr19-18482358;