rs12580476

Variant names:

• chr12-13391129-G-A
• rs12580476

Your query was ambiguous. Multiple possible variants found:

• chr12-13391129-G-A
• chr12-13391129-G-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 0.0991 in 152,152 control chromosomes in the GnomAD database, including 956 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 0.099 (956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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 (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0992 AC: 15083 AN: 152034 Hom.: 957 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0991 AC: 15073 AN: 152152 Hom.: 956 Cov.: 32 AF XY: 0.0987 AC XY: 7339 AN XY: 74386

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.101

Alfa AF: 0.124 Hom.: 637

Bravo AF: 0.0915

Asia WGS AF: 0.0750 AC: 263 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	3.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12580476; hg19: chr12-13544063;