rs4808801
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006532.4(ELL):c.744+1247T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,068 control chromosomes in the GnomAD database, including 16,657 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 0.44 ( 16657 hom., cov: 32)
Consequence
ELL
NM_006532.4 intron
NM_006532.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.114
Genes affected
ELL (HGNC:23114): (elongation factor for RNA polymerase II) Enables phosphatase binding activity. Involved in positive regulation of transcription, DNA-templated and snRNA transcription. Located in cytosol; nuclear body; and transcriptionally active chromatin. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELL | NM_006532.4 | c.744+1247T>C | intron_variant | ENST00000262809.9 | NP_006523.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELL | ENST00000262809.9 | c.744+1247T>C | intron_variant | 1 | NM_006532.4 | ENSP00000262809.3 | ||||
ELL | ENST00000596124.3 | c.345+1247T>C | intron_variant | 1 | ENSP00000475648.2 | |||||
ELL | ENST00000594635.6 | n.*579+1247T>C | intron_variant | 1 | ENSP00000475681.2 |
Frequencies
GnomAD3 genomes AF: 0.441 AC: 66938AN: 151950Hom.: 16624 Cov.: 32
GnomAD3 genomes
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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: 0.441 AC: 67022AN: 152068Hom.: 16657 Cov.: 32 AF XY: 0.439 AC XY: 32654AN XY: 74334
GnomAD4 genome
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67022
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32
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32654
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74334
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1404
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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