rs11940220

Variant names:

• chr4-69095222-T-C
• rs11940220
• ENST00000766360.1:n.710A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-69095222-T-C
• chr4-69095222-T-G

Variant summary

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

The ENST00000766360.1(ENSG00000299782):​n.710A>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 0.575 in 151,500 control chromosomes in the GnomAD database, including 26,047 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 (26047 hom., cov: 33)
• Consequence: ENSG00000299782 ENST00000766360.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 2 publications found

Genes affected

ENSG00000299782 (HGNC:):

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001349568.2	c.-26-3318T>C		intron_variant	Intron 2 of 6		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299782	ENST00000766360.1	n.710A>G		non_coding_transcript_exon_variant	Exon 4 of 4
UGT2B7	ENST00000502942.5	c.-26-3318T>C		intron_variant	Intron 2 of 5	2		ENSP00000426206.1
UGT2B7	ENST00000509763.1	n.260-3318T>C		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87083 AN: 151382 Hom.: 26001 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.575 AC: 87184 AN: 151500 Hom.: 26047 Cov.: 33 AF XY: 0.584 AC XY: 43203 AN XY: 73960

African (AFR) AF: 0.711 AC: 29335 AN: 41256

American (AMR) AF: 0.659 AC: 10022 AN: 15208

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

East Asian (EAS) AF: 0.699 AC: 3585 AN: 5126

South Asian (SAS) AF: 0.604 AC: 2913 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 5992 AN: 10486

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

European-Non Finnish (NFE) AF: 0.468 AC: 31706 AN: 67820

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

Alfa AF: 0.525 Hom.: 5361

Bravo AF: 0.590

Asia WGS AF: 0.656 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.24
PhyloP100		-3.2

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: rs11940220; hg19: chr4-69960940;