rs6706232

chr2-233729207-G-Achr2-233729207-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_019093.4(UGT1A3):c.81G>A(p.Glu27=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,613,822 control chromosomes in the GnomAD database, including 180,459 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 0.54 (23587 hom., cov: 33)
  • Exomes 𝑓: 0.46 (156872 hom.)
• Consequence: UGT1A3 NM_019093.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP7: Synonymous conserved (PhyloP=-0.614 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT1A3	NM_019093.4	c.81G>A	p.Glu27=	synonymous_variant	1/5	ENST00000482026.6
UGT1A6	NM_001072.4	c.861+35342G>A		intron_variant		ENST00000305139.11
UGT1A4	NM_007120.3	c.867+9520G>A		intron_variant		ENST00000373409.8
UGT1A10	NM_019075.4	c.856-37827G>A		intron_variant		ENST00000344644.10
UGT1A8	NM_019076.5	c.856-37827G>A		intron_variant		ENST00000373450.5
UGT1A7	NM_019077.3	c.856-37827G>A		intron_variant		ENST00000373426.4
UGT1A5	NM_019078.2	c.867+15349G>A		intron_variant		ENST00000373414.4
UGT1A9	NM_021027.3	c.856-37827G>A		intron_variant		ENST00000354728.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT1A3	ENST00000482026.6	c.81G>A	p.Glu27=	synonymous_variant	1/5	1	NM_019093.4	P1
UGT1A6	ENST00000305139.11	c.861+35342G>A		intron_variant		1	NM_001072.4	P1
UGT1A10	ENST00000344644.10	c.856-37827G>A		intron_variant		1	NM_019075.4	P1
UGT1A9	ENST00000354728.5	c.856-37827G>A		intron_variant		1	NM_021027.3	P1
UGT1A4	ENST00000373409.8	c.867+9520G>A		intron_variant		1	NM_007120.3	P1
UGT1A5	ENST00000373414.4	c.867+15349G>A		intron_variant		1	NM_019078.2	P1
UGT1A7	ENST00000373426.4	c.856-37827G>A		intron_variant		1	NM_019077.3	P1
UGT1A8	ENST00000373450.5	c.856-37827G>A		intron_variant		1	NM_019076.5	P1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81622 AN: 152014 Hom.: 23570 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.505

GnomAD3 exomes AF: 0.485 AC: 121965 AN: 251272 Hom.: 30930 AF XY: 0.487 AC XY: 66074 AN XY: 135810

Gnomad AFR exome AF: 0.766

Gnomad AMR exome AF: 0.464

Gnomad ASJ exome AF: 0.531

Gnomad EAS exome AF: 0.340

Gnomad SAS exome AF: 0.605

Gnomad FIN exome AF: 0.476

Gnomad NFE exome AF: 0.442

Gnomad OTH exome AF: 0.470

GnomAD4 exome AF: 0.457 AC: 667921 AN: 1461688 Hom.: 156872 Cov.: 104 AF XY: 0.461 AC XY: 335139 AN XY: 727144

Gnomad4 AFR exome AF: 0.766

Gnomad4 AMR exome AF: 0.468

Gnomad4 ASJ exome AF: 0.535

Gnomad4 EAS exome AF: 0.288

Gnomad4 SAS exome AF: 0.599

Gnomad4 FIN exome AF: 0.471

Gnomad4 NFE exome AF: 0.438

Gnomad4 OTH exome AF: 0.474

GnomAD4 genome AF: 0.537 AC: 81681 AN: 152134 Hom.: 23587 Cov.: 33 AF XY: 0.535 AC XY: 39774 AN XY: 74350

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.505

Alfa AF: 0.467 Hom.: 7268

Bravo AF: 0.543

Asia WGS AF: 0.471 AC: 1638 AN: 3478

EpiCase AF: 0.455

EpiControl AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.50
Dann	Benign	0.56

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: rs6706232; hg19: chr2-234637853; COSMIC: COSV59389206;