2-222809603-G-A

Position:

• chr2-222809603-G-A

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 0.707 in 152,034 control chromosomes in the GnomAD database, including 38,493 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 0.71 (38493 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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 (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.707 AC: 107359 AN: 151916 Hom.: 38442 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.707 AC: 107461 AN: 152034 Hom.: 38493 Cov.: 31 AF XY: 0.702 AC XY: 52151 AN XY: 74310

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.693

Alfa AF: 0.685 Hom.: 72405

Bravo AF: 0.710

Asia WGS AF: 0.609 AC: 2120 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	1.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6436346; hg19: chr2-223674322;