rs2396309

Variant names:

• chr2-226417449-C-G
• rs2396309

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 0.871 in 152,166 control chromosomes in the GnomAD database, including 57,847 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 0.87 (57847 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.871 AC: 132430 AN: 152048 Hom.: 57810 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.871 AC: 132522 AN: 152166 Hom.: 57847 Cov.: 31 AF XY: 0.874 AC XY: 65042 AN XY: 74392

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.888

Alfa AF: 0.865 Hom.: 7066

Bravo AF: 0.863

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2396309; hg19: chr2-227282165;