NM_001076.4:c.873+56A>T

Variant names:

• chr4-68667984-T-A
• rs2045100
• NM_001076.4:c.873+56A>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.873+56A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,598,726 control chromosomes in the GnomAD database, including 30,635 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 0.22 (4164 hom., cov: 32)
  • Exomes 𝑓: 0.18 (26471 hom.)
• Consequence: UGT2B15 NM_001076.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B15	NM_001076.4	c.873+56A>T		intron_variant	Intron 2 of 5	ENST00000338206.6	NP_001067.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B15	ENST00000338206.6	c.873+56A>T		intron_variant	Intron 2 of 5	1	NM_001076.4	ENSP00000341045.5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33697 AN: 151956 Hom.: 4149 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.179 AC: 259057 AN: 1446652 Hom.: 26471 AF XY: 0.177 AC XY: 127251 AN XY: 719574

African (AFR) AF: 0.264 AC: 8514 AN: 32308

American (AMR) AF: 0.414 AC: 16550 AN: 39930

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 5217 AN: 25560

East Asian (EAS) AF: 0.318 AC: 12572 AN: 39524

South Asian (SAS) AF: 0.140 AC: 11665 AN: 83532

European-Finnish (FIN) AF: 0.308 AC: 16378 AN: 53206

Middle Eastern (MID) AF: 0.215 AC: 1224 AN: 5684

European-Non Finnish (NFE) AF: 0.159 AC: 175656 AN: 1107110

Other (OTH) AF: 0.189 AC: 11281 AN: 59798

GnomAD4 genome AF: 0.222 AC: 33752 AN: 152074 Hom.: 4164 Cov.: 32 AF XY: 0.228 AC XY: 16980 AN XY: 74334

African (AFR) AF: 0.255 AC: 10582 AN: 41442

American (AMR) AF: 0.331 AC: 5062 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1509 AN: 5178

South Asian (SAS) AF: 0.140 AC: 673 AN: 4814

European-Finnish (FIN) AF: 0.314 AC: 3325 AN: 10576

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11249 AN: 68004

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.202 Hom.: 434

Bravo AF: 0.229

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-1.1
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: rs2045100; hg19: chr4-69533702; COSMIC: COSV57736197;