rs2391882

Variant names:

• chr13-110927204-C-G
• rs2391882

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 0.812 in 152,212 control chromosomes in the GnomAD database, including 50,431 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 0.81 (50431 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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: 0.812 AC: 123520 AN: 152094 Hom.: 50396 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.812 AC: 123610 AN: 152212 Hom.: 50431 Cov.: 33 AF XY: 0.813 AC XY: 60521 AN XY: 74418

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.831

Alfa AF: 0.825 Hom.: 6440

Bravo AF: 0.809

Asia WGS AF: 0.865 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391882; hg19: chr13-111579551;