rs1333583

Variant names:

• chr13-82565015-A-T
• rs1333583

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 0.518 in 151,976 control chromosomes in the GnomAD database, including 20,605 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 0.52 (20605 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 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: 0.518 AC: 78659 AN: 151860 Hom.: 20577 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.518 AC: 78736 AN: 151976 Hom.: 20605 Cov.: 31 AF XY: 0.518 AC XY: 38500 AN XY: 74264

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.485

Alfa AF: 0.516 Hom.: 2560

Bravo AF: 0.504

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333583; hg19: chr13-83139150;