5-134513486-C-G

Variant names:

• chr5-134513486-C-G
• rs13187289

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 0.187 in 149,422 control chromosomes in the GnomAD database, including 2,838 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 0.19 (2838 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

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 (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.187 AC: 27917 AN: 149312 Hom.: 2837 Cov.: 27

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.187 AC: 27930 AN: 149422 Hom.: 2838 Cov.: 27 AF XY: 0.184 AC XY: 13417 AN XY: 72780

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.194

Alfa AF: 0.183 Hom.: 1433

Bravo AF: 0.187

Asia WGS AF: 0.0830 AC: 289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13187289; hg19: chr5-133849177;