rs7435827

Variant names:

• chr4-68549226-A-G
• rs7435827
• NM_001077.4:c.1313+1451T>C

Variant summary

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

The NM_001077.4(UGT2B17):​c.1313+1451T>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 0.48 (22680 hom., cov: 19)
• Consequence: UGT2B17 NM_001077.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B17	NM_001077.4	MANE Select	c.1313+1451T>C		intron	N/A	NP_001068.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B17	ENST00000317746.3	TSL:1 MANE Select	c.1313+1451T>C		intron	N/A	ENSP00000320401.2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 58545 AN: 121320 Hom.: 22688 Cov.: 19

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.482 AC: 58525 AN: 121382 Hom.: 22680 Cov.: 19 AF XY: 0.477 AC XY: 27475 AN XY: 57578

African (AFR) AF: 0.170 AC: 6096 AN: 35932

American (AMR) AF: 0.490 AC: 5691 AN: 11608

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 1852 AN: 2914

East Asian (EAS) AF: 0.584 AC: 735 AN: 1258

South Asian (SAS) AF: 0.517 AC: 1307 AN: 2530

European-Finnish (FIN) AF: 0.561 AC: 3743 AN: 6670

Middle Eastern (MID) AF: 0.737 AC: 174 AN: 236

European-Non Finnish (NFE) AF: 0.650 AC: 37631 AN: 57914

Other (OTH) AF: 0.544 AC: 887 AN: 1630

Alfa AF: 0.509 Hom.: 2273

Asia WGS AF: 0.592 AC: 1101 AN: 1862

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.55
PhyloP100		1.9
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: rs7435827; hg19: chr4-69414944;