rs13394720

Variant names:

• chr2-233593475-T-C
• rs13394720

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 0.068 in 152,166 control chromosomes in the GnomAD database, including 556 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 0.068 (556 hom., cov: 32)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 12 publications found

Genes affected

UGT1A (HGNC:12529):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10310 AN: 152048 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0680 AC: 10348 AN: 152166 Hom.: 556 Cov.: 32 AF XY: 0.0675 AC XY: 5019 AN XY: 74410

African (AFR) AF: 0.152 AC: 6313 AN: 41498

American (AMR) AF: 0.0376 AC: 575 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3472

East Asian (EAS) AF: 0.0653 AC: 338 AN: 5176

South Asian (SAS) AF: 0.0339 AC: 163 AN: 4812

European-Finnish (FIN) AF: 0.0405 AC: 430 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2196 AN: 67994

Other (OTH) AF: 0.0600 AC: 127 AN: 2116

Alfa AF: 0.0440 Hom.: 645

Bravo AF: 0.0718

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.14
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs13394720; hg19: chr2-234502121;