rs9300319

chr12-111627093-T-Cchr12-111627093-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;