Variant 12-93410717-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_003348.4(UBE2N):c.418+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 1,613,750 control chromosomes in the GnomAD database, including 311 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 0.014 ( 24 hom., cov: 33)

Exomes 𝑓: 0.017 ( 287 hom. )

Consequence

UBE2N
NM_003348.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Variant links:

Genes affected

UBE2N (HGNC:12492): (ubiquitin conjugating enzyme E2 N) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Studies in mouse suggest that this protein plays a role in DNA postreplication repair. [provided by RefSeq, Jul 2008]

UBE2N links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0144 (2194/152334) while in subpopulation NFE AF= 0.0187 (1269/68040). AF 95% confidence interval is 0.0178. There are 24 homozygotes in gnomad4. There are 1089 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2194 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2N	NM_003348.4 linkuse as main transcript	c.418+17C>T		intron_variant		ENST00000318066.7	NP_003339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2N	ENST00000318066.7 linkuse as main transcript	c.418+17C>T		intron_variant		1	NM_003348.4	ENSP00000316176	P1

Frequencies

GnomAD3 genomes

AF:

0.0144

AC:

2195

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00376

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0164

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00517

Gnomad FIN

AF:

0.0225

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0186

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.0150

AC:

3756

AN:

250860

Hom.:

AF XY:

0.0152

AC XY:

2054

AN XY:

135544

show subpopulations

Gnomad AFR exome

AF:

0.00258

Gnomad AMR exome

AF:

0.0124

Gnomad ASJ exome

AF:

0.0255

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00663

Gnomad FIN exome

AF:

0.0224

Gnomad NFE exome

AF:

0.0196

Gnomad OTH exome

AF:

0.0196

GnomAD4 exome

AF:

0.0169

AC:

24771

AN:

1461416

Hom.:

287

Cov.:

AF XY:

0.0169

AC XY:

12302

AN XY:

726972

show subpopulations

Gnomad4 AFR exome

AF:

0.00332

Gnomad4 AMR exome

AF:

0.0126

Gnomad4 ASJ exome

AF:

0.0272

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00717

Gnomad4 FIN exome

AF:

0.0219

Gnomad4 NFE exome

AF:

0.0183

Gnomad4 OTH exome

AF:

0.0173

GnomAD4 genome

AF:

0.0144

AC:

2194

AN:

152334

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1089

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00375

Gnomad4 AMR

AF:

0.0164

Gnomad4 ASJ

AF:

0.0300

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.0225

Gnomad4 NFE

AF:

0.0187

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0170

Hom.:

Bravo

AF:

0.0136

Asia WGS

AF:

0.00375

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.69

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over