5-36047599-C-A

Variant names:

• chr5-36047599-C-A
• rs1287276
• NM_174914.4:c.843+1290G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174914.4(UGT3A2):​c.843+1290G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,062 control chromosomes in the GnomAD database, including 49,431 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 0.79 (49431 hom., cov: 31)
• Consequence: UGT3A2 NM_174914.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 3 publications found

Genes affected

UGT3A2 (HGNC:27266): (UDP glycosyltransferase family 3 member A2) Enables UDP-glycosyltransferase activity. Acts upstream of or within cellular response to genistein. 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174914.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT3A2	NM_174914.4	MANE Select	c.843+1290G>T		intron	N/A	NP_777574.2	Q3SY77-1
	UGT3A2	NM_001168316.2		c.741+1290G>T		intron	N/A	NP_001161788.1	Q3SY77-2
	UGT3A2	NR_031764.2		n.404+4271G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT3A2	ENST00000282507.8	TSL:1 MANE Select	c.843+1290G>T		intron	N/A	ENSP00000282507.3	Q3SY77-1
	UGT3A2	ENST00000926006.1		c.924+1290G>T		intron	N/A	ENSP00000596065.1
	UGT3A2	ENST00000513300.5	TSL:2	c.741+1290G>T		intron	N/A	ENSP00000427404.1	Q3SY77-2

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119492 AN: 151944 Hom.: 49422 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.813

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.786 AC: 119542 AN: 152062 Hom.: 49431 Cov.: 31 AF XY: 0.792 AC XY: 58890 AN XY: 74346

African (AFR) AF: 0.506 AC: 20950 AN: 41416

American (AMR) AF: 0.818 AC: 12495 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3078 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4140 AN: 5160

South Asian (SAS) AF: 0.969 AC: 4671 AN: 4818

European-Finnish (FIN) AF: 0.946 AC: 10027 AN: 10600

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61352 AN: 68000

Other (OTH) AF: 0.814 AC: 1717 AN: 2110

Alfa AF: 0.872 Hom.: 97756

Bravo AF: 0.763

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.18
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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: rs1287276; hg19: chr5-36047701;