dbSNP rs17147016: UGT2A3:c.*305A>T (chr4-68929508-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024743.4(UGT2A3):c.*305A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 214,190 control chromosomes in the GnomAD database, including 4,705 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 0.21 ( 3497 hom., cov: 32)

Exomes 𝑓: 0.18 ( 1208 hom. )

Consequence

UGT2A3
NM_024743.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

12 publications found

Variant links:

Genes affected

UGT2A3 (HGNC:28528): (UDP glucuronosyltransferase family 2 member A3) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

UGT2A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
UGT2A3	NM_024743.4 link	c.*305A>T	3_prime_UTR_variant	Exon 6 of 6	ENST00000251566.9	NP_079019.3
UGT2A3	NR_024010.2 link	n.2030A>T	non_coding_transcript_exon_variant	Exon 7 of 7
UGT2A3	XM_011532247.3 link	c.*305A>T	3_prime_UTR_variant	Exon 6 of 6		XP_011530549.1
UGT2A3	XM_047416177.1 link	c.*305A>T	3_prime_UTR_variant	Exon 6 of 6		XP_047272133.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
UGT2A3	ENST00000251566.9 link	c.*305A>T	3_prime_UTR_variant	Exon 6 of 6	1	NM_024743.4	ENSP00000251566.4
UGT2A3	ENST00000503012.1 link	n.*1065A>T	non_coding_transcript_exon_variant	Exon 7 of 7	2		ENSP00000424092.1
UGT2A3	ENST00000503012.1 link	n.*1065A>T	3_prime_UTR_variant	Exon 7 of 7	2		ENSP00000424092.1

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31935

AN:

151898

Hom.:

3497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.277

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.228

GnomAD4 exome

AF:

0.184

AC:

11433

AN:

62174

Hom.:

1208

Cov.:

AF XY:

0.181

AC XY:

5712

AN XY:

31516

show subpopulations

African (AFR)

AF:

0.205

AC:

511

AN:

2496

American (AMR)

AF:

0.170

AC:

634

AN:

3730

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

576

AN:

2192

East Asian (EAS)

AF:

0.307

AC:

1493

AN:

4868

South Asian (SAS)

AF:

0.124

AC:

282

AN:

2282

European-Finnish (FIN)

AF:

0.133

AC:

328

AN:

2470

Middle Eastern (MID)

AF:

0.234

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.170

AC:

6739

AN:

39684

Other (OTH)

AF:

0.193

AC:

797

AN:

4140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

439

878

1316

1755

2194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.210

AC:

31944

AN:

152016

Hom.:

3497

Cov.:

AF XY:

0.211

AC XY:

15687

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.243

AC:

10069

AN:

41452

American (AMR)

AF:

0.218

AC:

3321

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.295

AC:

1024

AN:

3468

East Asian (EAS)

AF:

0.340

AC:

1748

AN:

5136

South Asian (SAS)

AF:

0.177

AC:

855

AN:

4820

European-Finnish (FIN)

AF:

0.154

AC:

1630

AN:

10600

Middle Eastern (MID)

AF:

0.274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.185

AC:

12604

AN:

67966

Other (OTH)

AF:

0.225

AC:

476

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1286

2572

3858

5144

6430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

338

676

1014

1352

1690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.192

Hom.:

366

Bravo

AF:

0.221

Asia WGS

AF:

0.235

AC:

815

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.0

(source)

DANN

Benign

0.51

PhyloP100

-1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over