rs2215396

Variant names:

• chr12-126531637-A-G
• rs2215396

Your query was ambiguous. Multiple possible variants found:

• chr12-126531637-A-G
• chr12-126531637-A-T

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 0.671 in 152,036 control chromosomes in the GnomAD database, including 37,011 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 0.67 (37011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.671 AC: 101981 AN: 151918 Hom.: 36995 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.671 AC: 102038 AN: 152036 Hom.: 37011 Cov.: 32 AF XY: 0.679 AC XY: 50458 AN XY: 74322

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.677

Alfa AF: 0.748 Hom.: 40161

Bravo AF: 0.655

Asia WGS AF: 0.854 AC: 2965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215396; hg19: chr12-127016183;