rs12869406

Variant names:

• chr13-108234602-A-T
• rs12869406

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.146 AC: 6042 AN: 41490

American (AMR) AF: 0.172 AC: 2628 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3464

East Asian (EAS) AF: 0.109 AC: 562 AN: 5170

South Asian (SAS) AF: 0.0992 AC: 478 AN: 4818

European-Finnish (FIN) AF: 0.258 AC: 2711 AN: 10524

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15832 AN: 67852

Other (OTH) AF: 0.206 AC: 434 AN: 2110

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12869406; hg19: chr13-108886950;