12-87900706-A-G

Variant names:

• chr12-87900706-A-G
• rs2061589

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 0.702 in 151,920 control chromosomes in the GnomAD database, including 40,399 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 0.70 (40399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 (NFE) allele frequency at 95% confidence interval = 0.838 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: 0.702 AC: 106628 AN: 151802 Hom.: 40378 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.702 AC: 106691 AN: 151920 Hom.: 40399 Cov.: 31 AF XY: 0.704 AC XY: 52244 AN XY: 74236

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.748

Alfa AF: 0.800 Hom.: 22649

Bravo AF: 0.693

Asia WGS AF: 0.602 AC: 2094 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	0.079
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2061589; hg19: chr12-88294483;