4-69107416-CA-C

Variant names:

• chr4-69107416-CA-C
• rs11302069
• NM_001074.4:c.1090+155delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001074.4(UGT2B7):​c.1090+155delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27847 hom., cov: 0)
• Consequence: UGT2B7 NM_001074.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 2 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:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001074.4	c.1090+155delA		intron_variant	Intron 4 of 5	ENST00000305231.12	NP_001065.2
UGT2B7	NM_001330719.2	c.1090+155delA		intron_variant	Intron 4 of 4		NP_001317648.1
UGT2B7	NM_001349568.2	c.343+155delA		intron_variant	Intron 5 of 6		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12	c.1090+155delA		intron_variant	Intron 4 of 5	1	NM_001074.4	ENSP00000304811.7

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89604 AN: 151790 Hom.: 27798 Cov.: 0

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.591 AC: 89709 AN: 151908 Hom.: 27847 Cov.: 0 AF XY: 0.598 AC XY: 44422 AN XY: 74238

African (AFR) AF: 0.766 AC: 31738 AN: 41442

American (AMR) AF: 0.665 AC: 10162 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3464

East Asian (EAS) AF: 0.701 AC: 3618 AN: 5160

South Asian (SAS) AF: 0.555 AC: 2676 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6042 AN: 10528

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

European-Non Finnish (NFE) AF: 0.469 AC: 31817 AN: 67898

Other (OTH) AF: 0.599 AC: 1268 AN: 2116

Alfa AF: 0.333 Hom.: 726

Bravo AF: 0.607

Asia WGS AF: 0.638 AC: 2214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.9
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: rs11302069; hg19: chr4-69973134;