chr2-221224808-T-C

Position:

• chr2-221224808-T-C

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 0.239 in 151,686 control chromosomes in the GnomAD database, including 4,907 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 0.24 (4907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36231 AN: 151568 Hom.: 4891 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36274 AN: 151686 Hom.: 4907 Cov.: 32 AF XY: 0.238 AC XY: 17663 AN XY: 74200

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.261

Alfa AF: 0.207 Hom.: 877

Bravo AF: 0.258

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368065; hg19: chr2-222089528;