rs2870783

Variant names:

• chr12-66092543-A-G
• rs2870783

Your query was ambiguous. Multiple possible variants found:

• chr12-66092543-A-G
• chr12-66092543-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 0.445 in 150,060 control chromosomes in the GnomAD database, including 15,550 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 0.44 (15550 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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 (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.445 AC: 66665 AN: 149956 Hom.: 15525 Cov.: 28

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.445 AC: 66734 AN: 150060 Hom.: 15550 Cov.: 28 AF XY: 0.450 AC XY: 32904 AN XY: 73090

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.396

Alfa AF: 0.413 Hom.: 1615

Bravo AF: 0.435

Asia WGS AF: 0.663 AC: 2299 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
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: rs2870783; hg19: chr12-66486323;