chr4-69095621-G-A

Variant names:

• chr4-69095621-G-A
• rs7438135
• NM_001349568.2:c.-26-2919G>A

Variant summary

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

The NM_001349568.2(UGT2B7):​c.-26-2919G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,024 control chromosomes in the GnomAD database, including 26,336 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 (26336 hom., cov: 33)
• Consequence: UGT2B7 NM_001349568.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 61 publications found

Genes affected

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]

ENSG00000299782 (HGNC:58802):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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: NM_001349568.2. 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.-26-2919G>A		intron	N/A	NP_001336497.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B7	ENST00000502942.5	TSL:2	c.-26-2919G>A		intron	N/A	ENSP00000426206.1
	UGT2B7	ENST00000509763.1	TSL:5	n.260-2919G>A		intron	N/A
	ENSG00000299782	ENST00000766360.1		n.443-132C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87668 AN: 151906 Hom.: 26290 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.577 AC: 87769 AN: 152024 Hom.: 26336 Cov.: 33 AF XY: 0.586 AC XY: 43577 AN XY: 74320

African (AFR) AF: 0.713 AC: 29599 AN: 41514

American (AMR) AF: 0.660 AC: 10069 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1772 AN: 3462

East Asian (EAS) AF: 0.702 AC: 3622 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2916 AN: 4824

European-Finnish (FIN) AF: 0.576 AC: 6083 AN: 10568

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31852 AN: 67936

Other (OTH) AF: 0.590 AC: 1242 AN: 2106

Alfa AF: 0.516 Hom.: 58270

Bravo AF: 0.590

Asia WGS AF: 0.657 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.19
PhyloP100		-0.67

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: rs7438135; hg19: chr4-69961339;