rs1879390

Variant names:

• chr12-127433587-C-A
• rs1879390

Your query was ambiguous. Multiple possible variants found:

• chr12-127433587-C-A
• chr12-127433587-C-G
• chr12-127433587-C-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 0.14 in 152,044 control chromosomes in the GnomAD database, including 1,613 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 0.14 (1613 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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: 0.140 AC: 21312 AN: 151926 Hom.: 1606 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.140 AC: 21359 AN: 152044 Hom.: 1613 Cov.: 31 AF XY: 0.143 AC XY: 10625 AN XY: 74306

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0381

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.134

Alfa AF: 0.117 Hom.: 1534

Bravo AF: 0.137

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.41
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879390; hg19: chr12-127918132;