rs1333026

Variant names:

• chr13-65546652-A-G
• rs1333026

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 0.835 in 151,912 control chromosomes in the GnomAD database, including 53,161 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 0.83 (53161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.835 AC: 126717 AN: 151794 Hom.: 53126 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.835 AC: 126808 AN: 151912 Hom.: 53161 Cov.: 31 AF XY: 0.837 AC XY: 62177 AN XY: 74272

African (AFR) AF: 0.752 AC: 31154 AN: 41432

American (AMR) AF: 0.897 AC: 13661 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3097 AN: 3470

East Asian (EAS) AF: 0.929 AC: 4794 AN: 5162

South Asian (SAS) AF: 0.908 AC: 4386 AN: 4832

European-Finnish (FIN) AF: 0.852 AC: 9001 AN: 10564

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57754 AN: 67906

Other (OTH) AF: 0.857 AC: 1803 AN: 2104

Alfa AF: 0.848 Hom.: 231118

Bravo AF: 0.833

Asia WGS AF: 0.912 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.11
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1333026; hg19: chr13-66120784; COSMIC: COSV69359185;