rs2579103

chr12-90239730-C-A

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 0.783 in 152,026 control chromosomes in the GnomAD database, including 47,071 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 0.78 (47071 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.782 AC: 118863 AN: 151906 Hom.: 47006 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.783 AC: 118992 AN: 152026 Hom.: 47071 Cov.: 31 AF XY: 0.781 AC XY: 58011 AN XY: 74294

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.775

Alfa AF: 0.750 Hom.: 59732

Bravo AF: 0.790

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2579103; hg19: chr12-90633507;