rs2741023

Variant names:

• chr2-233608068-G-A
• rs2741023

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 0.261 in 152,086 control chromosomes in the GnomAD database, including 6,442 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 0.26 (6442 hom., cov: 32)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 10 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 (SAS) allele frequency at 95% confidence interval = 0.381 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: 0.261 AC: 39685 AN: 151968 Hom.: 6446 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.261 AC: 39672 AN: 152086 Hom.: 6442 Cov.: 32 AF XY: 0.264 AC XY: 19589 AN XY: 74322

African (AFR) AF: 0.0846 AC: 3514 AN: 41532

American (AMR) AF: 0.234 AC: 3577 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3470

East Asian (EAS) AF: 0.0281 AC: 146 AN: 5188

South Asian (SAS) AF: 0.396 AC: 1900 AN: 4804

European-Finnish (FIN) AF: 0.377 AC: 3968 AN: 10532

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24240 AN: 67964

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.328 Hom.: 14780

Bravo AF: 0.238

Asia WGS AF: 0.202 AC: 703 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	2.4
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2741023; hg19: chr2-234516714;