4-69095409-T-C

Variant names:

• chr4-69095409-T-C
• rs11940316
• ENST00000766360.1:n.523A>G

Variant summary

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

The ENST00000766360.1(ENSG00000299782):​n.523A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,096 control chromosomes in the GnomAD database, including 26,334 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 0.58 (26334 hom., cov: 33)
• Consequence: ENSG00000299782 ENST00000766360.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 11 publications found

Genes affected

ENSG00000299782 (HGNC:58802):

UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766360.1. 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
	UGT2B7	NM_001349568.2		c.-26-3131T>C		intron	N/A	NP_001336497.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299782	ENST00000766360.1		n.523A>G		non_coding_transcript_exon	Exon 4 of 4
	UGT2B7	ENST00000502942.5	TSL:2	c.-26-3131T>C		intron	N/A	ENSP00000426206.1
	UGT2B7	ENST00000509763.1	TSL:5	n.260-3131T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87659 AN: 151978 Hom.: 26288 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.577 AC: 87760 AN: 152096 Hom.: 26334 Cov.: 33 AF XY: 0.586 AC XY: 43566 AN XY: 74364

African (AFR) AF: 0.713 AC: 29586 AN: 41496

American (AMR) AF: 0.660 AC: 10066 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1773 AN: 3466

East Asian (EAS) AF: 0.701 AC: 3627 AN: 5174

South Asian (SAS) AF: 0.604 AC: 2919 AN: 4830

European-Finnish (FIN) AF: 0.574 AC: 6078 AN: 10588

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31849 AN: 67972

Other (OTH) AF: 0.588 AC: 1244 AN: 2116

Alfa AF: 0.514 Hom.: 57331

Bravo AF: 0.590

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.23
PhyloP100		-3.1

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: rs11940316; hg19: chr4-69961127;