rs1433251

chr12-72682251-A-Gchr12-72682251-A-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 0.47 in 151,294 control chromosomes in the GnomAD database, including 20,911 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 0.47 (20911 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.470 AC: 71009 AN: 151176 Hom.: 20860 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.470 AC: 71114 AN: 151294 Hom.: 20911 Cov.: 31 AF XY: 0.464 AC XY: 34295 AN XY: 73896

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.455

Alfa AF: 0.341 Hom.: 12836

Bravo AF: 0.507

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.60
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1433251; hg19: chr12-73076031; COSMIC: COSV70040898;