rs7004739
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173685.4(NSMCE2):c.419-41078G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,036 control chromosomes in the GnomAD database, including 17,609 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 0.45 ( 17609 hom., cov: 32)
Consequence
NSMCE2
NM_173685.4 intron
NM_173685.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.297
Genes affected
NSMCE2 (HGNC:26513): (NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase) This gene encodes a member of a family of E3 small ubiquitin-related modifier (SUMO) ligases that mediates the attachment of a SUMO protein to proteins involved in nuclear transport, transcription, chromosome segregation and DNA repair. The encoded protein is part of the structural maintenance of chromosomes (SMC) 5/6 complex which plays a key role genome maintenance, facilitating chromosome segregation and suppressing mitotic recombination. A knockout of the orthologous mouse gene is lethal prior to embryonic day 10.5. Naturally occurring mutations in this gene, that abolish the SUMO ligase activity, are associated with primordial dwarfism and extreme insulin resistance. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSMCE2 | NM_173685.4 | c.419-41078G>A | intron_variant | ENST00000287437.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSMCE2 | ENST00000287437.8 | c.419-41078G>A | intron_variant | 1 | NM_173685.4 | P1 | |||
NSMCE2 | ENST00000517315.1 | c.239-41078G>A | intron_variant | 3 | |||||
NSMCE2 | ENST00000517532.5 | c.419-41078G>A | intron_variant | 5 | |||||
NSMCE2 | ENST00000522563.5 | c.419-41078G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.448 AC: 68029AN: 151918Hom.: 17609 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.447 AC: 68030AN: 152036Hom.: 17609 Cov.: 32 AF XY: 0.450 AC XY: 33415AN XY: 74306
GnomAD4 genome
?
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68030
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32
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33415
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74306
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1487
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at