rs12337907

Variant names:

• chr9-21219602-G-T
• rs12337907

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 0.0846 in 151,964 control chromosomes in the GnomAD database, including 762 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 0.085 (762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0845 AC: 12826 AN: 151846 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0413

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0846 AC: 12852 AN: 151964 Hom.: 762 Cov.: 32 AF XY: 0.0831 AC XY: 6174 AN XY: 74296

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0413

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0618 Hom.: 82

Bravo AF: 0.0921

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12337907; hg19: chr9-21219601;