rs1287276

Positions:

• chr5-36047599-C-A
• chr5-36047599-C-G
• chr5-36047599-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT3A2	NM_174914.4	c.843+1290G>T		intron_variant		ENST00000282507.8	NP_777574.2
UGT3A2	NM_001168316.2	c.741+1290G>T		intron_variant			NP_001161788.1
UGT3A2	XM_011513988.2	c.924+1290G>T		intron_variant			XP_011512290.1
UGT3A2	NR_031764.2	n.404+4271G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT3A2	ENST00000282507.8	c.843+1290G>T		intron_variant		1	NM_174914.4	ENSP00000282507	P1
UGT3A2	ENST00000513300.5	c.741+1290G>T		intron_variant		2		ENSP00000427404
UGT3A2	ENST00000504685.5	c.311+4271G>T		intron_variant, NMD_transcript_variant		2		ENSP00000426017
UGT3A2	ENST00000504954.1	n.494+4271G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.814

Alfa AF: 0.884 Hom.: 78893

Bravo AF: 0.763

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.18

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: rs1287276; hg19: chr5-36047701;