Variant 1-202333104-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014176.4(UBE2T):c.385-11T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,611,924 control chromosomes in the GnomAD database, including 10,600 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 628 hom., cov: 31)

Exomes 𝑓: 0.11 ( 9972 hom. )

Consequence

UBE2T
NM_014176.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.04316

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.880

Variant links:

Genes affected

UBE2T (HGNC:25009): (ubiquitin conjugating enzyme E2 T) The protein encoded by this gene catalyzes the covalent attachment of ubiquitin to protein substrates. Defects in this gene have been associated with Fanconi anemia of complementation group T. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

UBE2T links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 1-202333104-A-G is Benign according to our data. Variant chr1-202333104-A-G is described in ClinVar as [Benign]. Clinvar id is 1231134.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2T	NM_014176.4 linkuse as main transcript	c.385-11T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000646651.1	NP_054895.1
UBE2T	NM_001310326.2 linkuse as main transcript	c.295-11T>C		splice_polypyrimidine_tract_variant, intron_variant			NP_001297255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2T	ENST00000646651.1 linkuse as main transcript	c.385-11T>C		splice_polypyrimidine_tract_variant, intron_variant			NM_014176.4	ENSP00000494957	P3

Frequencies

GnomAD3 genomes

AF:

0.0784

AC:

11912

AN:

151930

Hom.:

629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0226

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0614

Gnomad ASJ

AF:

0.0447

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.0991

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.0614

GnomAD3 exomes

AF:

0.0765

AC:

19237

AN:

251318

Hom.:

1040

AF XY:

0.0771

AC XY:

10479

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.0193

Gnomad AMR exome

AF:

0.0391

Gnomad ASJ exome

AF:

0.0477

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0152

Gnomad FIN exome

AF:

0.0959

Gnomad NFE exome

AF:

0.124

Gnomad OTH exome

AF:

0.0781

GnomAD4 exome

AF:

0.108

AC:

157499

AN:

1459876

Hom.:

9972

Cov.:

AF XY:

0.105

AC XY:

76477

AN XY:

726484

show subpopulations

Gnomad4 AFR exome

AF:

0.0172

Gnomad4 AMR exome

AF:

0.0421

Gnomad4 ASJ exome

AF:

0.0475

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0158

Gnomad4 FIN exome

AF:

0.0967

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.0868

GnomAD4 genome

AF:

0.0783

AC:

11907

AN:

152048

Hom.:

628

Cov.:

AF XY:

0.0753

AC XY:

5594

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.0225

Gnomad4 AMR

AF:

0.0613

Gnomad4 ASJ

AF:

0.0447

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0145

Gnomad4 FIN

AF:

0.0991

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.0607

Alfa

AF:

0.105

Hom.:

1632

Bravo

AF:

0.0732

Asia WGS

AF:

0.00953

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.043

dbscSNV1_RF

Benign

0.31

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over