rs1004202

Variant names:

• chr5-36065361-C-G
• rs1004202
• NM_174914.4:c.95-1011G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-36065361-C-G
• chr5-36065361-C-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.95-1011G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,012 control chromosomes in the GnomAD database, including 7,557 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 0.28 (7557 hom., cov: 31)
• Consequence: UGT3A2 NM_174914.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT3A2	NM_174914.4	c.95-1011G>C		intron_variant	Intron 1 of 6	ENST00000282507.8	NP_777574.2
UGT3A2	NM_001168316.2	c.94+1335G>C		intron_variant	Intron 1 of 5		NP_001161788.1
UGT3A2	NR_031764.2	n.188-1011G>C		intron_variant	Intron 1 of 5
UGT3A2	XM_011513988.2	c.95-1011G>C		intron_variant	Intron 1 of 7		XP_011512290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT3A2	ENST00000282507.8	c.95-1011G>C		intron_variant	Intron 1 of 6	1	NM_174914.4	ENSP00000282507.3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43000 AN: 151894 Hom.: 7563 Cov.: 31

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.283 AC: 42991 AN: 152012 Hom.: 7557 Cov.: 31 AF XY: 0.284 AC XY: 21080 AN XY: 74292

African (AFR) AF: 0.0757 AC: 3140 AN: 41484

American (AMR) AF: 0.324 AC: 4948 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5156

South Asian (SAS) AF: 0.262 AC: 1259 AN: 4814

European-Finnish (FIN) AF: 0.433 AC: 4568 AN: 10550

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26041 AN: 67954

Other (OTH) AF: 0.305 AC: 642 AN: 2108

Alfa AF: 0.0750 Hom.: 195

Bravo AF: 0.265

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		0.50
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: rs1004202; hg19: chr5-36065463;