rs9300319

Variant names:

• chr12-111627093-T-C
• rs9300319

Your query was ambiguous. Multiple possible variants found:

• chr12-111627093-T-C
• chr12-111627093-T-G

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 0.359 in 151,956 control chromosomes in the GnomAD database, including 14,325 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 0.36 (14325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.359 AC: 54436 AN: 151840 Hom.: 14285 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.359 AC: 54538 AN: 151956 Hom.: 14325 Cov.: 31 AF XY: 0.360 AC XY: 26710 AN XY: 74288

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.333

Alfa AF: 0.262 Hom.: 1132

Bravo AF: 0.392

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300319; hg19: chr12-112064897;