2-220938221-A-G

Variant names:

• chr2-220938221-A-G
• rs617222

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 0.339 in 151,988 control chromosomes in the GnomAD database, including 11,636 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 0.34 (11636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 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: 0.339 AC: 51464 AN: 151870 Hom.: 11597 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.339 AC: 51551 AN: 151988 Hom.: 11636 Cov.: 32 AF XY: 0.331 AC XY: 24583 AN XY: 74294

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.300

Alfa AF: 0.248 Hom.: 10463

Bravo AF: 0.353

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs617222; hg19: chr2-221802941;