rs12869406

Variant names:

• chr13-108234602-A-T
• rs12869406

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 0.196 in 151,910 control chromosomes in the GnomAD database, including 3,100 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 0.20 (3100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564

ACMG classification

Verdict is Benign. Variant got -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 = 0.23 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: 0.196 AC: 29695 AN: 151792 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.196 AC: 29728 AN: 151910 Hom.: 3100 Cov.: 32 AF XY: 0.195 AC XY: 14446 AN XY: 74266

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.206

Alfa AF: 0.224 Hom.: 520

Bravo AF: 0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12869406; hg19: chr13-108886950;