rs12039309

Variant names:

• chr1-111050747-T-G
• rs12039309

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 0.217 in 151,814 control chromosomes in the GnomAD database, including 4,234 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 (4234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.217 AC: 32918 AN: 151696 Hom.: 4237 Cov.: 31

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.217 AC: 32916 AN: 151814 Hom.: 4234 Cov.: 31 AF XY: 0.219 AC XY: 16216 AN XY: 74214

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.206

Alfa AF: 0.241 Hom.: 606

Bravo AF: 0.202

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12039309; hg19: chr1-111593369;