rs12487870

Variant names:

• chr3-1510024-G-A
• rs12487870

Your query was ambiguous. Multiple possible variants found:

• chr3-1510024-G-A
• chr3-1510024-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0882 in 151,584 control chromosomes in the GnomAD database, including 789 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 0.088 (789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0882 AC: 13364 AN: 151466 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0882 AC: 13375 AN: 151584 Hom.: 789 Cov.: 32 AF XY: 0.0857 AC XY: 6348 AN XY: 74034

African (AFR) AF: 0.0417 AC: 1726 AN: 41382

American (AMR) AF: 0.0754 AC: 1144 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3468

East Asian (EAS) AF: 0.000390 AC: 2 AN: 5124

South Asian (SAS) AF: 0.0329 AC: 158 AN: 4804

European-Finnish (FIN) AF: 0.105 AC: 1092 AN: 10444

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8568 AN: 67870

Other (OTH) AF: 0.109 AC: 229 AN: 2106

Alfa AF: 0.0810 Hom.: 217

Bravo AF: 0.0872

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.71
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs12487870; hg19: chr3-1551708;