rs2882302

Positions:

• chr14-59871628-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;