rs12580476

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;