chr4-68567230-T-C

Position:

• chr4-68567230-T-C

Variant summary

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

The NM_001077.4(UGT2B17):​c.724+531A>G 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 0.98 (59689 hom., cov: 20)
• Consequence: UGT2B17 NM_001077.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT2B17	NM_001077.4	c.724+531A>G		intron_variant		ENST00000317746.3	NP_001068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B17	ENST00000317746.3	c.724+531A>G		intron_variant		1	NM_001077.4	ENSP00000320401	P1
UGT2B17	ENST00000684088.1	c.-26-1510A>G		intron_variant				ENSP00000507374

Frequencies

GnomAD3 genomes AF: 0.978 AC: 120772 AN: 123472 Hom.: 59656 Cov.: 20

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.992

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.978 AC: 120839 AN: 123540 Hom.: 59689 Cov.: 20 AF XY: 0.977 AC XY: 57452 AN XY: 58826

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.988

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.987

Alfa AF: 0.987 Hom.: 5981

Asia WGS AF: 0.995 AC: 1850 AN: 1860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.55

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: rs6552182; hg19: chr4-69432948;