rs12380341

Variant names:

• chr9-104969287-C-T
• rs12380341

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 0.166 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• 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

African (AFR) AF: 0.168 AC: 6975 AN: 41548

American (AMR) AF: 0.135 AC: 2055 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3472

East Asian (EAS) AF: 0.151 AC: 784 AN: 5178

South Asian (SAS) AF: 0.138 AC: 668 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11708 AN: 67990

Other (OTH) AF: 0.162 AC: 342 AN: 2110

Alfa AF: 0.167 Hom.: 6833

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
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs12380341; hg19: chr9-107731568;