rs3100

Variant names:

• chr4-68646936-G-A
• rs3100
• NM_001076.4:c.*168C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-68646936-G-A
• chr4-68646936-G-C
• chr4-68646936-G-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.*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
• Publications: 23 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

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>T		3_prime_UTR	Exon 6 of 6	NP_001067.2

Ensembl Transcripts

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

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

African (AFR) AF: 0.223 AC: 4358 AN: 19548

American (AMR) AF: 0.536 AC: 10498 AN: 19576

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 9877 AN: 15988

East Asian (EAS) AF: 0.172 AC: 5836 AN: 33896

South Asian (SAS) AF: 0.522 AC: 26670 AN: 51054

European-Finnish (FIN) AF: 0.629 AC: 26720 AN: 42462

Middle Eastern (MID) AF: 0.553 AC: 1536 AN: 2776

European-Non Finnish (NFE) AF: 0.658 AC: 412896 AN: 627506

Other (OTH) AF: 0.576 AC: 22335 AN: 38746

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

African (AFR) AF: 0.235 AC: 9469 AN: 40290

American (AMR) AF: 0.519 AC: 7801 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2142 AN: 3452

East Asian (EAS) AF: 0.187 AC: 932 AN: 4984

South Asian (SAS) AF: 0.526 AC: 2490 AN: 4738

European-Finnish (FIN) AF: 0.628 AC: 6520 AN: 10380

Middle Eastern (MID) AF: 0.552 AC: 160 AN: 290

European-Non Finnish (NFE) AF: 0.647 AC: 43760 AN: 67598

Other (OTH) AF: 0.481 AC: 998 AN: 2076

Alfa AF: 0.563 Hom.: 21787

Bravo AF: 0.469

Asia WGS AF: 0.370 AC: 1268 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.17
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: rs3100; hg19: chr4-69512654;