rs2066575
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NR_109974.1(DLEU1):n.278T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 470,932 control chromosomes in the GnomAD database, including 11,976 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 0.20 ( 3597 hom., cov: 32)
Exomes 𝑓: 0.22 ( 8379 hom. )
Consequence
DLEU1
NR_109974.1 non_coding_transcript_exon
NR_109974.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0300
Genes affected
DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)
DLEU2 (HGNC:13748): (deleted in lymphocytic leukemia 2) This locus represents a microRNA host gene and also produces long alternatively spliced non-coding RNAs. This genome region was observed to be deleted or epigenetically suppressed in leukemia, and was implicated as a negative regulator of cell proliferation. However, an alternative transcript produced at this locus was also found to promote progression through the cell cycle via angiotensin I converting enzyme 2 and cyclin D1. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLEU1 | NR_109974.1 | n.278T>A | non_coding_transcript_exon_variant | 1/7 | |||
DLEU2 | NR_152566.1 | n.241-6793A>T | intron_variant, non_coding_transcript_variant | ||||
DLEU1 | NR_002605.2 | n.278T>A | non_coding_transcript_exon_variant | 1/2 | |||
DLEU1 | NR_109973.1 | n.278T>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLEU1 | ENST00000490577.5 | n.276T>A | non_coding_transcript_exon_variant | 1/6 | 5 | ||||
ENST00000618107.1 | n.152T>A | non_coding_transcript_exon_variant | 1/1 | ||||||
DLEU2 | ENST00000621282.4 | n.241-6793A>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.198 AC: 30126AN: 152076Hom.: 3599 Cov.: 32
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GnomAD3 exomes AF: 0.219 AC: 33250AN: 151586Hom.: 3985 AF XY: 0.216 AC XY: 17621AN XY: 81434
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GnomAD4 exome AF: 0.220 AC: 69964AN: 318738Hom.: 8379 Cov.: 0 AF XY: 0.212 AC XY: 38249AN XY: 180048
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GnomAD4 genome ? AF: 0.198 AC: 30141AN: 152194Hom.: 3597 Cov.: 32 AF XY: 0.197 AC XY: 14679AN XY: 74414
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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