rs1597944

Variant names:

• chr2-233595452-C-T
• rs1597944

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 0.444 in 151,950 control chromosomes in the GnomAD database, including 16,577 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 0.44 (16577 hom., cov: 31)
• Consequence: UGT1A intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 7 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 (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67387 AN: 151832 Hom.: 16572 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.444 AC: 67419 AN: 151950 Hom.: 16577 Cov.: 31 AF XY: 0.451 AC XY: 33514 AN XY: 74246

African (AFR) AF: 0.220 AC: 9109 AN: 41454

American (AMR) AF: 0.478 AC: 7295 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2776 AN: 5150

South Asian (SAS) AF: 0.661 AC: 3175 AN: 4800

European-Finnish (FIN) AF: 0.523 AC: 5521 AN: 10556

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35939 AN: 67930

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.506 Hom.: 37908

Bravo AF: 0.425

Asia WGS AF: 0.580 AC: 2013 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	2.2
DANN	Benign	0.17
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1597944; hg19: chr2-234504098;