2-233729061-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019093.4(UGT1A3):c.-66T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,610,256 control chromosomes in the GnomAD database, including 184,343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

• Frequency:
  • Genomes: 𝑓 0.55 (25689 hom., cov: 33)
  • Exomes 𝑓: 0.46 (158654 hom.)
• Consequence: UGT1A3 NM_019093.4 5_prime_UTR
• Clinical Significance: other no assertion criteria provided O:1
• Conservation: PhyloP100: -4.45

Genes affected

UGT1A3 (HGNC:12535): (UDP glucuronosyltransferase family 1 member A3) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. Substrates of this enzyme include estrone, 2-hydroxyestrone, and metabolites of benzo alpha-pyrene. [provided by RefSeq, Jul 2008]

UGT1A6 (HGNC:12538): (UDP glucuronosyltransferase family 1 member A6) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene is active on phenolic and planar compounds. Alternative splicing in the unique 5' end of this gene results in two transcript variants. [provided by RefSeq, Jul 2008]

UGT1A4 (HGNC:12536): (UDP glucuronosyltransferase family 1 member A4) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. This enzyme has some glucuronidase activity towards bilirubin, although is is more active on amines, steroids, and sapogenins. [provided by RefSeq, Jul 2008]

UGT1A10 (HGNC:12531): (UDP glucuronosyltransferase family 1 member A10) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity on mycophenolic acid, coumarins, and quinolines. [provided by RefSeq, Jul 2008]

UGT1A8 (HGNC:12540): (UDP glucuronosyltransferase family 1 member A8) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity with many substrates including coumarins, phenols, anthraquinones, flavones, and some opioids. [provided by RefSeq, Jul 2008]

UGT1A7 (HGNC:12539): (UDP glucuronosyltransferase family 1 member A7) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has moderate glucuronidase activity with phenols. [provided by RefSeq, Jul 2008]

UGT1A5 (HGNC:12537): (UDP glucuronosyltransferase family 1 member A5) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. [provided by RefSeq, Jul 2008]

UGT1A9 (HGNC:12541): (UDP glucuronosyltransferase family 1 member A9) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene is active on phenols. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT1A3	NM_019093.4	c.-66T>C		5_prime_UTR_variant	1/5	ENST00000482026.6
UGT1A6	NM_001072.4	c.861+35196T>C		intron_variant		ENST00000305139.11
UGT1A4	NM_007120.3	c.867+9374T>C		intron_variant		ENST00000373409.8
UGT1A10	NM_019075.4	c.856-37973T>C		intron_variant		ENST00000344644.10
UGT1A8	NM_019076.5	c.856-37973T>C		intron_variant		ENST00000373450.5
UGT1A7	NM_019077.3	c.856-37973T>C		intron_variant		ENST00000373426.4
UGT1A5	NM_019078.2	c.867+15203T>C		intron_variant		ENST00000373414.4
UGT1A9	NM_021027.3	c.856-37973T>C		intron_variant		ENST00000354728.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT1A3	ENST00000482026.6	c.-66T>C		5_prime_UTR_variant	1/5	1	NM_019093.4	P1
UGT1A6	ENST00000305139.11	c.861+35196T>C		intron_variant		1	NM_001072.4	P1
UGT1A10	ENST00000344644.10	c.856-37973T>C		intron_variant		1	NM_019075.4	P1
UGT1A9	ENST00000354728.5	c.856-37973T>C		intron_variant		1	NM_021027.3	P1
UGT1A4	ENST00000373409.8	c.867+9374T>C		intron_variant		1	NM_007120.3	P1
UGT1A5	ENST00000373414.4	c.867+15203T>C		intron_variant		1	NM_019078.2	P1
UGT1A7	ENST00000373426.4	c.856-37973T>C		intron_variant		1	NM_019077.3	P1
UGT1A8	ENST00000373450.5	c.856-37973T>C		intron_variant		1	NM_019076.5	P1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84356 AN: 152104 Hom.: 25643 Cov.: 33

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.515

GnomAD4 exome AF: 0.459 AC: 669360 AN: 1458036 Hom.: 158654 Cov.: 55 AF XY: 0.463 AC XY: 335625 AN XY: 725180

Gnomad4 AFR exome AF: 0.832

Gnomad4 AMR exome AF: 0.472

Gnomad4 ASJ exome AF: 0.543

Gnomad4 EAS exome AF: 0.288

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.472

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.479

GnomAD4 genome AF: 0.555 AC: 84450 AN: 152220 Hom.: 25689 Cov.: 33 AF XY: 0.553 AC XY: 41128 AN XY: 74412

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.516

Alfa AF: 0.512 Hom.: 3399

Bravo AF: 0.563

Asia WGS AF: 0.478 AC: 1663 AN: 3478

ClinVar

Significance: other

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Levothyroxine response Other:1

other, no assertion criteria provided

research

Pharmacogenomics/Precision medicine lab, University of Petra

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- The TT genotype of this SNP in our study was associated with lower levels of T4 after levothyroxine replacement

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.095
Dann	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806596; hg19: chr2-234637707; COSMIC: COSV59390325; COSMIC: COSV59390325;