rs9300244

Variant names:

• chr12-13996137-G-C
• rs9300244

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 0.301 in 152,022 control chromosomes in the GnomAD database, including 8,484 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 0.30 (8484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.301 AC: 45772 AN: 151904 Hom.: 8490 Cov.: 33

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.301 AC: 45771 AN: 152022 Hom.: 8484 Cov.: 33 AF XY: 0.307 AC XY: 22786 AN XY: 74322

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.327

Alfa AF: 0.317 Hom.: 1076

Bravo AF: 0.300

Asia WGS AF: 0.520 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.091
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300244; hg19: chr12-14149071;