2-233612023-T-G

Variant names:

• chr2-233612023-T-G
• rs4281899

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 0.257 in 152,066 control chromosomes in the GnomAD database, including 5,388 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 (5388 hom., cov: 31)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.257 AC: 39036 AN: 151946 Hom.: 5378 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.257 AC: 39074 AN: 152066 Hom.: 5388 Cov.: 31 AF XY: 0.258 AC XY: 19150 AN XY: 74350

African (AFR) AF: 0.215 AC: 8926 AN: 41464

American (AMR) AF: 0.306 AC: 4677 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2671 AN: 5166

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4816

European-Finnish (FIN) AF: 0.196 AC: 2070 AN: 10588

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17588 AN: 67964

Other (OTH) AF: 0.274 AC: 578 AN: 2106

Alfa AF: 0.145 Hom.: 275

Bravo AF: 0.264

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.21
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4281899; hg19: chr2-234520669;