rs12578896

Variant names:

• chr12-131279829-G-A
• rs12578896

Your query was ambiguous. Multiple possible variants found:

• chr12-131279829-G-A
• chr12-131279829-G-C

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 0.383 in 151,888 control chromosomes in the GnomAD database, including 11,845 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 0.38 (11845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.383 AC: 58117 AN: 151770 Hom.: 11845 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.383 AC: 58128 AN: 151888 Hom.: 11845 Cov.: 33 AF XY: 0.382 AC XY: 28379 AN XY: 74220

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.385

Alfa AF: 0.420 Hom.: 17326

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12578896; hg19: chr12-131764374;