rs282273

Variant names:

• chr2-224058305-C-A
• rs282273

Your query was ambiguous. Multiple possible variants found:

• chr2-224058305-C-A
• chr2-224058305-C-G
• chr2-224058305-C-T

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 0.431 in 151,994 control chromosomes in the GnomAD database, including 18,258 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 0.43 (18258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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: 0.430 AC: 65346 AN: 151876 Hom.: 18193 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.431 AC: 65476 AN: 151994 Hom.: 18258 Cov.: 32 AF XY: 0.428 AC XY: 31817 AN XY: 74276

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.387

Alfa AF: 0.345 Hom.: 2355

Bravo AF: 0.453

Asia WGS AF: 0.475 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282273; hg19: chr2-224923022;