Genetic Variant UGT2B15:c.*168C>A (chr4-68646936-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001076.4(UGT2B15):c.*168C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

UGT2B15
NM_001076.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

23 publications found

Variant links:

Genes affected

UGT2B15 (HGNC:12546): (UDP glucuronosyltransferase family 2 member B15) This gene encodes a glycosyltransferase that is invovled in the metabolism and elimination of toxic compounts, both endogenous and of xenobiotic origin. This gene plays a role in the regulation of estrogens and androgens. This locus is present in a cluster of similar genes and pseudogenes on chromosome 4. [provided by RefSeq, Aug 2016]

UGT2B15 links:

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ACMG classification

Classification was made for transcript

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=-1.03).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001076.4. 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
	UGT2B15	NM_001076.4	MANE Select	c.*168C>A		3_prime_UTR	Exon 6 of 6	NP_001067.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UGT2B15	ENST00000338206.6	TSL:1 MANE Select	c.*168C>A	3_prime_UTR	Exon 6 of 6	ENSP00000341045.5
UGT2B15	ENST00000962480.1		c.*168C>A	3_prime_UTR	Exon 5 of 5	ENSP00000632539.1
UGT2B15	ENST00000871508.1		c.*168C>A	3_prime_UTR	Exon 6 of 6	ENSP00000541567.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

854726

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

428070

African (AFR)

AF:

0.00

AC:

AN:

19596

American (AMR)

AF:

0.00

AC:

AN:

19616

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16030

East Asian (EAS)

AF:

0.00

AC:

AN:

33934

South Asian (SAS)

AF:

0.00

AC:

AN:

51344

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42572

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2784

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

629986

Other (OTH)

AF:

0.00

AC:

AN:

38864

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

21787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

(source)

DANN

Benign

0.20

PhyloP100

-1.1

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over