Genetic Variant UBR7:c.*41C>T (chr14-93227076-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175748.4(UBR7):c.*41C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,459,678 control chromosomes in the GnomAD database, including 71,536 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 0.24 ( 5667 hom., cov: 32)

Exomes 𝑓: 0.31 ( 65869 hom. )

Consequence

UBR7
NM_175748.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.671

Publications

40 publications found

Variant links:

Genes affected

UBR7 (HGNC:20344): (ubiquitin protein ligase E3 component n-recognin 7) This gene encodes a UBR box-containing protein that belongs to the E3 ubiquitin ligase family. The protein also contains a plant homeodomain (PHD) in the C-terminus. In mammals, the encoded protein recognizes N-degrons, the destabilizing N-terminal residues of short-lived proteins, which results in ubiquitinylation, and proteolysis via the proteasome. [provided by RefSeq, Jul 2016]

UBR7 Gene-Disease associations (from GenCC):

Li-Campeau syndrome
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
intellectual disability
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

UBR7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBR7	NM_175748.4 link	c.*41C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000013070.11	NP_786924.2
UBR7	NR_038150.2 link	n.1221C>T		non_coding_transcript_exon_variant	Exon 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBR7	ENST00000013070.11 link	c.*41C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_175748.4	ENSP00000013070.6		Q8N806

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37148

AN:

151916

Hom.:

5670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0660

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.327

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.249

GnomAD2 exomes

AF:

0.279

AC:

68487

AN:

245880

AF XY:

0.279

show subpopulations

Gnomad AFR exome

AF:

0.0603

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.342

Gnomad EAS exome

AF:

0.268

Gnomad FIN exome

AF:

0.318

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.288

GnomAD4 exome

AF:

0.310

AC:

405656

AN:

1307644

Hom.:

65869

Cov.:

AF XY:

0.307

AC XY:

202225

AN XY:

658334

show subpopulations

African (AFR)

AF:

0.0544

AC:

1634

AN:

30056

American (AMR)

AF:

0.257

AC:

11289

AN:

43974

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

8387

AN:

24864

East Asian (EAS)

AF:

0.246

AC:

9390

AN:

38130

South Asian (SAS)

AF:

0.179

AC:

14785

AN:

82486

European-Finnish (FIN)

AF:

0.321

AC:

16359

AN:

50998

Middle Eastern (MID)

AF:

0.258

AC:

1406

AN:

5452

European-Non Finnish (NFE)

AF:

0.334

AC:

326116

AN:

976928

Other (OTH)

AF:

0.298

AC:

16290

AN:

54756

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

12304

24609

36913

49218

61522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.244

AC:

37140

AN:

152034

Hom.:

5667

Cov.:

AF XY:

0.246

AC XY:

18269

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0658

AC:

2731

AN:

41496

American (AMR)

AF:

0.292

AC:

4459

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

1136

AN:

3470

East Asian (EAS)

AF:

0.250

AC:

1291

AN:

5160

South Asian (SAS)

AF:

0.173

AC:

833

AN:

4812

European-Finnish (FIN)

AF:

0.319

AC:

3368

AN:

10554

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.331

AC:

22514

AN:

67952

Other (OTH)

AF:

0.247

AC:

520

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1344

2689

4033

5378

6722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.307

Hom.:

16590

Bravo

AF:

0.233

Asia WGS

AF:

0.210

AC:

731

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.67

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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chr14-93227076-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over