5-35963405-T-G

Variant names:

• chr5-35963405-T-G
• rs700162
• NM_152404.4:c.843+1981A>C

Variant summary

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

The NM_152404.4(UGT3A1):​c.843+1981A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,014 control chromosomes in the GnomAD database, including 11,277 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 0.36 (11277 hom., cov: 32)
• Consequence: UGT3A1 NM_152404.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 4 publications found

Genes affected

UGT3A1 (HGNC:26625): (UDP glycosyltransferase family 3 member A1) Enables glucuronosyltransferase activity. Part of UDP-N-acetylglucosamine transferase complex. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152404.4. 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
	UGT3A1	NM_152404.4	MANE Select	c.843+1981A>C		intron	N/A	NP_689617.3
	UGT3A1	NM_001171873.2		c.682-454A>C		intron	N/A	NP_001165344.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT3A1	ENST00000274278.8	TSL:1 MANE Select	c.843+1981A>C		intron	N/A	ENSP00000274278.3
	UGT3A1	ENST00000625798.2	TSL:1	c.682-454A>C		intron	N/A	ENSP00000487376.1
	UGT3A1	ENST00000503189.5	TSL:2	c.843+1981A>C		intron	N/A	ENSP00000427079.1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54017 AN: 151896 Hom.: 11270 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.356 AC: 54048 AN: 152014 Hom.: 11277 Cov.: 32 AF XY: 0.363 AC XY: 26945 AN XY: 74298

African (AFR) AF: 0.160 AC: 6635 AN: 41488

American (AMR) AF: 0.482 AC: 7361 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3875 AN: 5154

South Asian (SAS) AF: 0.579 AC: 2790 AN: 4818

European-Finnish (FIN) AF: 0.382 AC: 4035 AN: 10556

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26917 AN: 67944

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.286 Hom.: 1081

Bravo AF: 0.352

Asia WGS AF: 0.585 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.80
PhyloP100		0.27
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: rs700162; hg19: chr5-35963507;