rs2391882

chr13-110927204-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;