rs12280580

chr11-626220-C-Gchr11-626220-C-T

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 0.296 in 594,092 control chromosomes in the GnomAD database, including 29,699 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 0.35 (10656 hom., cov: 32)
  • Exomes 𝑓: 0.28 (19043 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.351 AC: 53368 AN: 151982 Hom.: 10645 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.276 AC: 122194 AN: 441992 Hom.: 19043 AF XY: 0.270 AC XY: 62563 AN XY: 231530

Gnomad4 AFR exome AF: 0.531

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.362

Gnomad4 EAS exome AF: 0.0222

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.245

Gnomad4 NFE exome AF: 0.305

Gnomad4 OTH exome AF: 0.297

GnomAD4 genome AF: 0.351 AC: 53404 AN: 152100 Hom.: 10656 Cov.: 32 AF XY: 0.341 AC XY: 25339 AN XY: 74358

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.346

Alfa AF: 0.222 Hom.: 511

Bravo AF: 0.369

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12280580; hg19: chr11-626220;