rs7969431
Positions:
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
NM_003348.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.121
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]
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 | UniProt |
---|---|---|---|---|---|---|---|
UBE2N | NM_003348.4 | c.418+17C>T | intron_variant | ENST00000318066.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2N | ENST00000318066.7 | c.418+17C>T | intron_variant | 1 | NM_003348.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0144 AC: 2195AN: 152216Hom.: 24 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
2195
AN:
152216
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0150 AC: 3756AN: 250860Hom.: 44 AF XY: 0.0152 AC XY: 2054AN XY: 135544
GnomAD3 exomes
AF:
AC:
3756
AN:
250860
Hom.:
AF XY:
AC XY:
2054
AN XY:
135544
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0169 AC: 24771AN: 1461416Hom.: 287 Cov.: 31 AF XY: 0.0169 AC XY: 12302AN XY: 726972
GnomAD4 exome
AF:
AC:
24771
AN:
1461416
Hom.:
Cov.:
31
AF XY:
AC XY:
12302
AN XY:
726972
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0144 AC: 2194AN: 152334Hom.: 24 Cov.: 33 AF XY: 0.0146 AC XY: 1089AN XY: 74486
GnomAD4 genome
?
AF:
AC:
2194
AN:
152334
Hom.:
Cov.:
33
AF XY:
AC XY:
1089
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
13
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at