4-69496023-A-T

Variant names:

• chr4-69496023-A-T
• rs941389
• ENST00000968901.1:c.-42-120T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001297616.2(UGT2B4):​c.44-613T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,088,326 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: UGT2B4 NM_001297616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297616.2. 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
	UGT2B4	NM_001297616.2		c.44-613T>A		intron	N/A	NP_001284545.1
	UGT2B4	NM_021139.3	MANE Select	c.-162T>A		upstream_gene	N/A	NP_066962.2
	UGT2B4	NM_001297615.2		c.-162T>A		upstream_gene	N/A	NP_001284544.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B4	ENST00000968901.1		c.-42-120T>A		intron	N/A	ENSP00000638960.1
	UGT2B4	ENST00000510114.1	TSL:4	c.-105-57T>A		intron	N/A	ENSP00000421113.1
	UGT2B4	ENST00000502655.5	TSL:5	n.329-613T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000276 AC: 3 AN: 1088326 Hom.: 0 AF XY: 0.00000561 AC XY: 3 AN XY: 534968

African (AFR) AF: 0.00 AC: 0 AN: 23848

American (AMR) AF: 0.00 AC: 0 AN: 19982

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17066

East Asian (EAS) AF: 0.00 AC: 0 AN: 33846

South Asian (SAS) AF: 0.0000210 AC: 1 AN: 47668

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33044

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4694

European-Non Finnish (NFE) AF: 0.00000232 AC: 2 AN: 861794

Other (OTH) AF: 0.00 AC: 0 AN: 46384

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.23
DANN	Benign	0.37
PhyloP100		-0.41
PromoterAI		-0.030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs941389; hg19: chr4-70361741;