rs13133830

Variant names:

• chr4-141542965-G-A
• rs13133830

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 0.114 in 152,110 control chromosomes in the GnomAD database, including 1,239 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 0.11 (1239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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: 0.115 AC: 17406 AN: 151992 Hom.: 1240 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.114 AC: 17408 AN: 152110 Hom.: 1239 Cov.: 32 AF XY: 0.114 AC XY: 8490 AN XY: 74358

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.125

Alfa AF: 0.134 Hom.: 241

Bravo AF: 0.110

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.036
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: rs13133830; hg19: chr4-142464118;