rs2391882

Variant names:

• chr13-110927204-C-G
• rs2391882

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.727 AC: 30168 AN: 41494

American (AMR) AF: 0.838 AC: 12816 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3118 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4754 AN: 5184

South Asian (SAS) AF: 0.812 AC: 3918 AN: 4826

European-Finnish (FIN) AF: 0.837 AC: 8869 AN: 10592

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57132 AN: 68026

Other (OTH) AF: 0.831 AC: 1754 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2391882; hg19: chr13-111579551;