rs12999373

chr2-663483-G-Achr2-663483-G-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 0.222 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;