rs2282424

Variant names:

• chr13-97136192-G-A
• rs2282424

Your query was ambiguous. Multiple possible variants found:

• chr13-97136192-G-A
• chr13-97136192-G-C

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 0.099 in 152,120 control chromosomes in the GnomAD database, including 870 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 0.099 (870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0990 AC: 15050 AN: 152002 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0990 AC: 15061 AN: 152120 Hom.: 870 Cov.: 32 AF XY: 0.103 AC XY: 7630 AN XY: 74350

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0721 Hom.: 521

Bravo AF: 0.100

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282424; hg19: chr13-97788446;