rs12380341

Variant names:

• chr9-104969287-C-T
• rs12380341

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 0.166 in 152,190 control chromosomes in the GnomAD database, including 2,123 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 0.17 (2123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.166 AC: 25223 AN: 152072 Hom.: 2127 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.166 AC: 25227 AN: 152190 Hom.: 2123 Cov.: 32 AF XY: 0.166 AC XY: 12329 AN XY: 74396

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.162

Alfa AF: 0.168 Hom.: 4488

Bravo AF: 0.161

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12380341; hg19: chr9-107731568;