chr2-663483-G-A

Variant names:

• chr2-663483-G-A
• rs12999373

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 0.222 in 152,190 control chromosomes in the GnomAD database, including 4,099 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 0.22 (4099 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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 (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.222 AC: 33828 AN: 152072 Hom.: 4099 Cov.: 34

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.222 AC: 33834 AN: 152190 Hom.: 4099 Cov.: 34 AF XY: 0.224 AC XY: 16649 AN XY: 74386

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0461

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.243

Alfa AF: 0.249 Hom.: 7137

Bravo AF: 0.212

Asia WGS AF: 0.119 AC: 415 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	0.42
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12999373; hg19: chr2-663483;