chr2-49830251-C-T

Variant names:

• chr2-49830251-C-T
• rs17039353

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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.331

Alfa AF: 0.336 Hom.: 4308

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17039353; hg19: chr2-50057389;