rs12378245

Variant names:

• chr9-110628663-T-C
• rs12378245

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 0.134 in 152,086 control chromosomes in the GnomAD database, including 1,562 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 0.13 (1562 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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: 0.134 AC: 20290 AN: 151968 Hom.: 1560 Cov.: 33

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.134 AC: 20308 AN: 152086 Hom.: 1562 Cov.: 33 AF XY: 0.133 AC XY: 9876 AN XY: 74338

Gnomad4 AFR AF: 0.0788

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.142

Alfa AF: 0.151 Hom.: 303

Bravo AF: 0.126

Asia WGS AF: 0.0630 AC: 220 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12378245; hg19: chr9-113390943;