rs3880457
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002904.6(NELFE):c.1046-44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,451,042 control chromosomes in the GnomAD database, including 97 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 0.0019 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 89 hom. )
Consequence
NELFE
NM_002904.6 intron
NM_002904.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.22
Genes affected
NELFE (HGNC:13974): (negative elongation factor complex member E) The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]
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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=-0.93).
BA1
?
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0643 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NELFE | NM_002904.6 | c.1046-44A>G | intron_variant | ENST00000375429.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELFE | ENST00000375429.8 | c.1046-44A>G | intron_variant | 1 | NM_002904.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00191 AC: 291AN: 152144Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00362 AC: 826AN: 228360Hom.: 18 AF XY: 0.00332 AC XY: 411AN XY: 123810
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GnomAD4 exome AF: 0.00217 AC: 2816AN: 1298780Hom.: 89 Cov.: 18 AF XY: 0.00215 AC XY: 1406AN XY: 653696
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GnomAD4 genome ? AF: 0.00194 AC: 296AN: 152262Hom.: 8 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74454
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at