rs10784293

Positions:

• chr12-62417548-A-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 0.267 in 158,986 control chromosomes in the GnomAD database, including 6,989 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 0.27 (6638 hom., cov: 32)
  • Exomes 𝑓: 0.30 (351 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.266 AC: 40445 AN: 151964 Hom.: 6631 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.299 AC: 2067 AN: 6904 Hom.: 351 AF XY: 0.297 AC XY: 1092 AN XY: 3682

Gnomad4 AFR exome AF: 0.0735

Gnomad4 AMR exome AF: 0.300

Gnomad4 ASJ exome AF: 0.324

Gnomad4 EAS exome AF: 0.417

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.454

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.316

GnomAD4 genome AF: 0.266 AC: 40452 AN: 152082 Hom.: 6638 Cov.: 32 AF XY: 0.274 AC XY: 20376 AN XY: 74334

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.248

Alfa AF: 0.302 Hom.: 3464

Bravo AF: 0.249

Asia WGS AF: 0.300 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10784293; hg19: chr12-62811328;