rs13129471

Variant names:

• chr4-69496405-G-A
• rs13129471
• NM_001297616.2:c.44-995C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-69496405-G-A
• chr4-69496405-G-C

Variant summary

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

The NM_001297616.2(UGT2B4):​c.44-995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,988 control chromosomes in the GnomAD database, including 26,470 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 0.58 (26470 hom., cov: 32)
• Consequence: UGT2B4 NM_001297616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 3 publications found

Genes affected

UGT2B4 (HGNC:12553): (UDP glucuronosyltransferase family 2 member B4) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation and estrogen metabolic process. Predicted to be located in endoplasmic reticulum membrane. 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B4	NM_001297616.2	c.44-995C>T		intron_variant	Intron 1 of 6		NP_001284545.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B4	ENST00000510114.1	c.-105-439C>T		intron_variant	Intron 1 of 1	4		ENSP00000421113.1
UGT2B4	ENST00000502655.5	n.329-995C>T		intron_variant	Intron 1 of 5	5
UGT2B4	ENST00000503836.5	n.329-2564C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88079 AN: 151870 Hom.: 26457 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.580 AC: 88133 AN: 151988 Hom.: 26470 Cov.: 32 AF XY: 0.587 AC XY: 43635 AN XY: 74280

African (AFR) AF: 0.408 AC: 16921 AN: 41444

American (AMR) AF: 0.663 AC: 10105 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2269 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3859 AN: 5156

South Asian (SAS) AF: 0.662 AC: 3191 AN: 4822

European-Finnish (FIN) AF: 0.681 AC: 7189 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42539 AN: 67982

Other (OTH) AF: 0.601 AC: 1266 AN: 2108

Alfa AF: 0.582 Hom.: 7345

Bravo AF: 0.571

Asia WGS AF: 0.681 AC: 2367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.39
PhyloP100		0.25
PromoterAI		0.020	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13129471; hg19: chr4-70362123;