rs289068

Variant names:

• chr12-66268223-C-T
• rs289068

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 0.767 in 151,974 control chromosomes in the GnomAD database, including 44,692 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 0.77 (44692 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.767 AC: 116532 AN: 151856 Hom.: 44646 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.767 AC: 116637 AN: 151974 Hom.: 44692 Cov.: 30 AF XY: 0.772 AC XY: 57307 AN XY: 74264

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.766

Alfa AF: 0.763 Hom.: 10968

Bravo AF: 0.769

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs289068; hg19: chr12-66662003;