rs7441750

Variant names:

• chr4-69098803-G-A
• rs7441750
• NM_001074.4:c.870+115G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-69098803-G-A
• chr4-69098803-G-C
• chr4-69098803-G-T

Variant summary

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

The NM_001074.4(UGT2B7):​c.870+115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,532,098 control chromosomes in the GnomAD database, including 196,687 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 (26290 hom., cov: 32)
  • Exomes 𝑓: 0.49 (170397 hom.)
• Consequence: UGT2B7 NM_001074.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• 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:58802):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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_001074.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B7	NM_001074.4	MANE Select	c.870+115G>A		intron	N/A	NP_001065.2	P16662
	UGT2B7	NM_001330719.2		c.870+115G>A		intron	N/A	NP_001317648.1	E9PBP8
	UGT2B7	NM_001349568.2		c.123+115G>A		intron	N/A	NP_001336497.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B7	ENST00000305231.12	TSL:1 MANE Select	c.870+115G>A		intron	N/A	ENSP00000304811.7	P16662
	UGT2B7	ENST00000868341.1		c.870+115G>A		intron	N/A	ENSP00000538400.1
	UGT2B7	ENST00000868343.1		c.870+115G>A		intron	N/A	ENSP00000538402.1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87528 AN: 151666 Hom.: 26244 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.588

GnomAD4 exome AF: 0.490 AC: 676963 AN: 1380314 Hom.: 170397 AF XY: 0.492 AC XY: 337457 AN XY: 686172

African (AFR) AF: 0.717 AC: 21304 AN: 29732

American (AMR) AF: 0.696 AC: 21102 AN: 30340

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 11552 AN: 22644

East Asian (EAS) AF: 0.703 AC: 27272 AN: 38814

South Asian (SAS) AF: 0.565 AC: 42678 AN: 75584

European-Finnish (FIN) AF: 0.579 AC: 29707 AN: 51342

Middle Eastern (MID) AF: 0.534 AC: 2327 AN: 4360

European-Non Finnish (NFE) AF: 0.459 AC: 491761 AN: 1070726

Other (OTH) AF: 0.515 AC: 29260 AN: 56772

GnomAD4 genome AF: 0.577 AC: 87629 AN: 151784 Hom.: 26290 Cov.: 32 AF XY: 0.586 AC XY: 43477 AN XY: 74162

African (AFR) AF: 0.713 AC: 29577 AN: 41474

American (AMR) AF: 0.660 AC: 10031 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3615 AN: 5148

South Asian (SAS) AF: 0.604 AC: 2907 AN: 4810

European-Finnish (FIN) AF: 0.576 AC: 6070 AN: 10546

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

European-Non Finnish (NFE) AF: 0.469 AC: 31796 AN: 67818

Other (OTH) AF: 0.588 AC: 1242 AN: 2112

Alfa AF: 0.398 Hom.: 1195

Bravo AF: 0.590

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0060
DANN	Benign	0.74
PhyloP100		-0.18
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: rs7441750; hg19: chr4-69964521;