chr2-220938221-A-G

Position:

• chr2-220938221-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;