rs2741027

Variant names:

• chr2-233609365-G-A
• rs2741027

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 0.224 in 152,078 control chromosomes in the GnomAD database, including 4,743 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 0.22 (4743 hom., cov: 32)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 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: 0.224 AC: 34016 AN: 151960 Hom.: 4745 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.224 AC: 34012 AN: 152078 Hom.: 4743 Cov.: 32 AF XY: 0.229 AC XY: 17046 AN XY: 74322

African (AFR) AF: 0.0765 AC: 3173 AN: 41492

American (AMR) AF: 0.194 AC: 2972 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3470

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5176

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3670 AN: 10544

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20107 AN: 67972

Other (OTH) AF: 0.216 AC: 456 AN: 2114

Alfa AF: 0.280 Hom.: 10669

Bravo AF: 0.200

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2741027; hg19: chr2-234518011;