rs7434408

chr4-68553552-A-G

Variant summary

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

The NM_001077.4(UGT2B17):c.1006-1641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.47 (22581 hom., cov: 20)
• Consequence: UGT2B17 NM_001077.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

UGT2B17 (HGNC:12547): (UDP glucuronosyltransferase family 2 member B17) This gene encodes a member of the uridine diphosphoglucuronosyltransferase protein family. The encoded enzyme catalyzes the transfer of glucuronic acid from uridine diphosphoglucuronic acid to a diverse array of substrates including steroid hormones and lipid-soluble drugs. This process, known as glucuronidation, is an intermediate step in the metabolism of steroids. Copy number variation in this gene is associated with susceptibility to osteoporosis.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT2B17	NM_001077.4	c.1006-1641T>C		intron_variant		ENST00000317746.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2B17	ENST00000317746.3	c.1006-1641T>C		intron_variant		1	NM_001077.4	P1
UGT2B17	ENST00000684088.1	c.256-1641T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.466 AC: 57561 AN: 123610 Hom.: 22589 Cov.: 20

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.743

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.528

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.465 AC: 57541 AN: 123678 Hom.: 22581 Cov.: 20 AF XY: 0.460 AC XY: 27105 AN XY: 58914

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.533

Alfa AF: 0.491 Hom.: 2135

Asia WGS AF: 0.587 AC: 1109 AN: 1892

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.1
Dann	Benign	0.87

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: rs7434408; hg19: chr4-69419270;