rs12489521

Positions:

• chr3-30342573-A-G

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 0.851 in 151,874 control chromosomes in the GnomAD database, including 55,426 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 0.85 (55426 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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: 0.851 AC: 129167 AN: 151756 Hom.: 55369 Cov.: 30

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.851 AC: 129286 AN: 151874 Hom.: 55426 Cov.: 30 AF XY: 0.854 AC XY: 63362 AN XY: 74214

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.828

Alfa AF: 0.802 Hom.: 71390

Bravo AF: 0.855

Asia WGS AF: 0.904 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.032
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12489521; hg19: chr3-30384065;