rs17039353

Variant names:

• chr2-49830251-C-T
• rs17039353

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 0.342 in 152,098 control chromosomes in the GnomAD database, including 9,413 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 0.34 (9413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.342 AC: 51938 AN: 151980 Hom.: 9398 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.342 AC: 51998 AN: 152098 Hom.: 9413 Cov.: 33 AF XY: 0.336 AC XY: 25014 AN XY: 74356

African (AFR) AF: 0.448 AC: 18578 AN: 41476

American (AMR) AF: 0.243 AC: 3722 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21707 AN: 67974

Other (OTH) AF: 0.331 AC: 700 AN: 2114

Alfa AF: 0.337 Hom.: 4804

Bravo AF: 0.343

Asia WGS AF: 0.341 AC: 1187 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	0.17
DANN	Benign	0.56
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs17039353; hg19: chr2-50057389;