rs12874278
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109974.1(DLEU1):n.443-28412C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 472,988 control chromosomes in the GnomAD database, including 1,053 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 0.064 ( 365 hom., cov: 32)
Exomes 𝑓: 0.061 ( 688 hom. )
Consequence
DLEU1
NR_109974.1 intron, non_coding_transcript
NR_109974.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.271
Genes affected
DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)
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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=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLEU1 | NR_109974.1 | n.443-28412C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLEU1 | ENST00000490577.5 | n.1638-71627C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
RPL34P26 | ENST00000445636.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0643 AC: 9779AN: 152058Hom.: 358 Cov.: 32
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GnomAD4 exome AF: 0.0613 AC: 19673AN: 320812Hom.: 688 Cov.: 0 AF XY: 0.0635 AC XY: 11542AN XY: 181858
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GnomAD4 genome ? AF: 0.0644 AC: 9805AN: 152176Hom.: 365 Cov.: 32 AF XY: 0.0633 AC XY: 4711AN XY: 74404
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at