2-233718617-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The NM_019078.2(UGT1A5):c.867+4759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 870,400 control chromosomes in the GnomAD database, including 378 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.028 (58 hom., cov: 33)
  • Exomes 𝑓: 0.029 (320 hom.)
• Consequence: UGT1A5 NM_019078.2 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.981

Genes affected

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]

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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.028 (4265/152296) while in subpopulation AFR AF= 0.0339 (1408/41578). AF 95% confidence interval is 0.0324. There are 58 homozygotes in gnomad4. There are 2007 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT1A6	NM_001072.4	c.861+24752G>A		intron_variant		ENST00000305139.11
UGT1A10	NM_019075.4	c.856-48417G>A		intron_variant		ENST00000344644.10
UGT1A8	NM_019076.5	c.856-48417G>A		intron_variant		ENST00000373450.5
UGT1A7	NM_019077.3	c.855+35825G>A		intron_variant		ENST00000373426.4
UGT1A5	NM_019078.2	c.867+4759G>A		intron_variant		ENST00000373414.4
UGT1A9	NM_021027.3	c.855+45828G>A		intron_variant		ENST00000354728.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT1A6	ENST00000305139.11	c.861+24752G>A		intron_variant		1	NM_001072.4	P1
UGT1A10	ENST00000344644.10	c.856-48417G>A		intron_variant		1	NM_019075.4	P1
UGT1A9	ENST00000354728.5	c.855+45828G>A		intron_variant		1	NM_021027.3	P1
UGT1A5	ENST00000373414.4	c.867+4759G>A		intron_variant		1	NM_019078.2	P1
UGT1A7	ENST00000373426.4	c.855+35825G>A		intron_variant		1	NM_019077.3	P1
UGT1A8	ENST00000373450.5	c.856-48417G>A		intron_variant		1	NM_019076.5	P1

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4263 AN: 152178 Hom.: 58 Cov.: 33

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0268

GnomAD4 exome AF: 0.0289 AC: 20744 AN: 718104 Hom.: 320 AF XY: 0.0288 AC XY: 9597 AN XY: 333808

Gnomad4 AFR exome AF: 0.0286

Gnomad4 AMR exome AF: 0.0146

Gnomad4 ASJ exome AF: 0.0414

Gnomad4 EAS exome AF: 0.000968

Gnomad4 SAS exome AF: 0.00603

Gnomad4 FIN exome AF: 0.0328

Gnomad4 NFE exome AF: 0.0296

Gnomad4 OTH exome AF: 0.0255

GnomAD4 genome AF: 0.0280 AC: 4265 AN: 152296 Hom.: 58 Cov.: 33 AF XY: 0.0269 AC XY: 2007 AN XY: 74480

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0309

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0158 Hom.: 5

Bravo AF: 0.0281

Asia WGS AF: 0.00924 AC: 32 AN: 3476

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Dec 31, 2014

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.4
Dann	Benign	0.66

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: rs45454101; hg19: chr2-234627263; COSMIC: COSV59392069; COSMIC: COSV59392069;