rs4148271

Variant names:

• chr4-68646919-T-A
• rs4148271
• NM_001076.4:c.*185A>T

Variant summary

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

The NM_001076.4(UGT2B15):​c.*185A>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 0.0347 in 766,254 control chromosomes in the GnomAD database, including 1,570 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 0.090 (281 hom., cov: 32)
  • Exomes 𝑓: 0.031 (1289 hom.)
• Consequence: UGT2B15 NM_001076.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B15	NM_001076.4	c.*185A>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000338206.6	NP_001067.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B15	ENST00000338206.6	c.*185A>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_001076.4	ENSP00000341045.5

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 4225 AN: 47184 Hom.: 281 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.0311 AC: 22382 AN: 719020 Hom.: 1289 Cov.: 9 AF XY: 0.0327 AC XY: 11854 AN XY: 362956

African (AFR) AF: 0.00816 AC: 145 AN: 17776

American (AMR) AF: 0.0532 AC: 959 AN: 18030

Ashkenazi Jewish (ASJ) AF: 0.0367 AC: 551 AN: 15002

East Asian (EAS) AF: 0.237 AC: 7666 AN: 32316

South Asian (SAS) AF: 0.0747 AC: 3450 AN: 46200

European-Finnish (FIN) AF: 0.0175 AC: 649 AN: 37192

Middle Eastern (MID) AF: 0.0626 AC: 157 AN: 2506

European-Non Finnish (NFE) AF: 0.0144 AC: 7403 AN: 515644

Other (OTH) AF: 0.0408 AC: 1402 AN: 34354

GnomAD4 genome AF: 0.0895 AC: 4229 AN: 47234 Hom.: 281 Cov.: 32 AF XY: 0.0989 AC XY: 2274 AN XY: 22994

African (AFR) AF: 0.0187 AC: 339 AN: 18084

American (AMR) AF: 0.222 AC: 824 AN: 3720

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 152 AN: 1248

East Asian (EAS) AF: 0.476 AC: 1345 AN: 2824

South Asian (SAS) AF: 0.321 AC: 378 AN: 1178

European-Finnish (FIN) AF: 0.0913 AC: 152 AN: 1664

Middle Eastern (MID) AF: 0.139 AC: 15 AN: 108

European-Non Finnish (NFE) AF: 0.0527 AC: 924 AN: 17536

Other (OTH) AF: 0.156 AC: 100 AN: 640

Alfa AF: 0.0243 Hom.: 117

Bravo AF: 0.0306

Asia WGS AF: 0.142 AC: 486 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.50
PhyloP100		-0.10
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: rs4148271; hg19: chr4-69512637; COSMIC: COSV57734064;