2-224055459-C-T

Variant names:

• chr2-224055459-C-T
• rs282268

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 0.415 in 152,014 control chromosomes in the GnomAD database, including 16,456 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 (16456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.415 AC: 62973 AN: 151896 Hom.: 16392 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.415 AC: 63102 AN: 152014 Hom.: 16456 Cov.: 32 AF XY: 0.413 AC XY: 30716 AN XY: 74318

African (AFR) AF: 0.743 AC: 30789 AN: 41452

American (AMR) AF: 0.336 AC: 5132 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2673 AN: 5172

South Asian (SAS) AF: 0.317 AC: 1523 AN: 4808

European-Finnish (FIN) AF: 0.298 AC: 3149 AN: 10570

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17477 AN: 67960

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.294 Hom.: 23031

Bravo AF: 0.435

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs282268; hg19: chr2-224920176;