rs2882302

Variant names:

• chr14-59871628-A-G
• rs2882302

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 0.417 in 152,144 control chromosomes in the GnomAD database, including 14,167 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 0.42 (14167 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -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 = 0.621 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: 0.417 AC: 63419 AN: 152024 Hom.: 14138 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.417 AC: 63508 AN: 152144 Hom.: 14167 Cov.: 33 AF XY: 0.417 AC XY: 31047 AN XY: 74382

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.452

Alfa AF: 0.397 Hom.: 1168

Bravo AF: 0.431

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882302; hg19: chr14-60338346;