rs1333583

Variant names:

• chr13-82565015-A-T
• rs1333583

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.550 AC: 22792 AN: 41440

American (AMR) AF: 0.434 AC: 6624 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1602 AN: 3460

East Asian (EAS) AF: 0.612 AC: 3155 AN: 5158

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4814

European-Finnish (FIN) AF: 0.578 AC: 6106 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34375 AN: 67964

Other (OTH) AF: 0.485 AC: 1021 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1333583; hg19: chr13-83139150;