chr2-233593475-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT1A		n.233593475T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;