2-221224796-A-T

Position:

• chr2-221224796-A-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 0.226 in 151,726 control chromosomes in the GnomAD database, including 4,292 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 0.23 (4292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

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 (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34191 AN: 151606 Hom.: 4278 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.226 AC: 34230 AN: 151726 Hom.: 4292 Cov.: 32 AF XY: 0.224 AC XY: 16637 AN XY: 74236

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.250

Alfa AF: 0.202 Hom.: 407

Bravo AF: 0.243

Asia WGS AF: 0.332 AC: 1156 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	7.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368064; hg19: chr2-222089516;