rs2882302

Variant names:

• chr14-59871628-A-G
• rs2882302

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 0.417 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.559 AC: 23184 AN: 41502

American (AMR) AF: 0.404 AC: 6182 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3297 AN: 5160

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4820

European-Finnish (FIN) AF: 0.263 AC: 2789 AN: 10586

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23217 AN: 67996

Other (OTH) AF: 0.452 AC: 952 AN: 2108

Alfa AF: 0.394 Hom.: 2579

Bravo AF: 0.431

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.46
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs2882302; hg19: chr14-60338346;