rs13128286

Variant names:

• chr4-68929908-C-G
• rs13128286
• NM_024743.4:c.1489G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-68929908-C-G
• chr4-68929908-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024743.4(UGT2A3):​c.1489G>C​(p.Ala497Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: UGT2A3 NM_024743.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024743.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2A3	NM_024743.4	MANE Select	c.1489G>C	p.Ala497Pro	missense	Exon 6 of 6	NP_079019.3
	UGT2A3	NR_024010.2		n.1630G>C		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2A3	ENST00000251566.9	TSL:1 MANE Select	c.1489G>C	p.Ala497Pro	missense	Exon 6 of 6	ENSP00000251566.4
	UGT2A3	ENST00000503012.1	TSL:2	n.*665G>C		non_coding_transcript_exon	Exon 7 of 7	ENSP00000424092.1
	UGT2A3	ENST00000503012.1	TSL:2	n.*665G>C		3_prime_UTR	Exon 7 of 7	ENSP00000424092.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 50

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Uncertain	0.026	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	18
DANN	Uncertain	1.0
DEOGEN2	Benign	0.35	T
Eigen	Benign	-0.026
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.057	N
M_CAP	Benign	0.0093	T
MetaRNN	Uncertain	0.71	D
MetaSVM	Benign	-0.76	T
MutationAssessor	Pathogenic	3.8	H
PhyloP100		0.28
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-3.8	D
REVEL	Benign	0.27
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0050	D
Polyphen		1.0	D
Vest4		0.34
MutPred		0.75		Loss of stability (P = 0.1909)
MVP		0.69
MPC		0.023
ClinPred		0.92	D
GERP RS		2.2
Varity_R		0.59
gMVP		0.48
Mutation Taster		=85/15	polymorphism

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

Other links and lift over

dbSNP: rs13128286; hg19: chr4-69795626;