rs3100

Positions:

• chr4-68646936-G-A
• chr4-68646936-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001076.4(UGT2B15):​c.*168C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 149,736 control chromosomes in the GnomAD database, including 21,322 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 0.50 (21322 hom., cov: 31)
  • Exomes 𝑓: 0.61 (163336 hom.)
  • Failed GnomAD Quality Control
• Consequence: UGT2B15 NM_001076.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT2B15	NM_001076.4	c.*168C>T		3_prime_UTR_variant	6/6	ENST00000338206.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2B15	ENST00000338206.6	c.*168C>T		3_prime_UTR_variant	6/6	1	NM_001076.4	P1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 74850 AN: 149624 Hom.: 21320 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.483

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.612 AC: 520726 AN: 851552 Hom.: 163336 Cov.: 11 AF XY: 0.610 AC XY: 260089 AN XY: 426426

Gnomad4 AFR exome AF: 0.223

Gnomad4 AMR exome AF: 0.536

Gnomad4 ASJ exome AF: 0.618

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.522

Gnomad4 FIN exome AF: 0.629

Gnomad4 NFE exome AF: 0.658

Gnomad4 OTH exome AF: 0.576

GnomAD4 genome AF: 0.500 AC: 74879 AN: 149736 Hom.: 21322 Cov.: 31 AF XY: 0.498 AC XY: 36364 AN XY: 73016

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.481

Alfa AF: 0.577 Hom.: 5604

Bravo AF: 0.469

Asia WGS AF: 0.370 AC: 1268 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.17

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

LitVar

Other links and lift over

dbSNP: rs3100; hg19: chr4-69512654;