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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT1A		n.233600317C>T		intragenic_variant

Ensembl

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

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 v4.3

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;