rs902215

Variant names:

• chr11-1643386-C-A
• rs902215

Your query was ambiguous. Multiple possible variants found:

• chr11-1643386-C-A
• chr11-1643386-C-G
• chr11-1643386-C-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 0.776 in 151,896 control chromosomes in the GnomAD database, including 45,880 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 0.78 (45880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.776 AC: 117815 AN: 151778 Hom.: 45852 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.776 AC: 117892 AN: 151896 Hom.: 45880 Cov.: 31 AF XY: 0.780 AC XY: 57913 AN XY: 74252

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.772

Alfa AF: 0.787 Hom.: 9510

Bravo AF: 0.769

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs902215; hg19: chr11-1664616;