rs2741012

Variant names:

• chr2-233600317-C-T
• rs2741012

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 0.242 in 152,152 control chromosomes in the GnomAD database, including 5,042 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 0.24 (5042 hom., cov: 32)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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: 0.242 AC: 36821 AN: 152034 Hom.: 5043 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.242 AC: 36818 AN: 152152 Hom.: 5042 Cov.: 32 AF XY: 0.246 AC XY: 18328 AN XY: 74368

African (AFR) AF: 0.142 AC: 5898 AN: 41522

American (AMR) AF: 0.200 AC: 3062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3468

East Asian (EAS) AF: 0.0279 AC: 145 AN: 5190

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4826

European-Finnish (FIN) AF: 0.348 AC: 3676 AN: 10574

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

European-Non Finnish (NFE) AF: 0.296 AC: 20122 AN: 67976

Other (OTH) AF: 0.230 AC: 486 AN: 2112

Alfa AF: 0.282 Hom.: 18402

Bravo AF: 0.222

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2741012; hg19: chr2-234508963;