rs3118905
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000460525.6(DLEU1):n.363-1995G>A 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 0.21 in 151,508 control chromosomes in the GnomAD database, including 3,940 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 0.21 ( 3940 hom., cov: 32)
Consequence
DLEU1
ENST00000460525.6 intron, non_coding_transcript
ENST00000460525.6 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.03
Genes affected
DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLEU1 | ENST00000460525.6 | n.363-1995G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
DLEU1 | ENST00000462427.2 | n.452-1995G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
DLEU7 | ENST00000651397.1 | c.*572-5191C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.210 AC: 31817AN: 151390Hom.: 3940 Cov.: 32
GnomAD3 genomes
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31817
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151390
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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: 0.210 AC: 31819AN: 151508Hom.: 3940 Cov.: 32 AF XY: 0.209 AC XY: 15437AN XY: 74016
GnomAD4 genome
?
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AC:
31819
AN:
151508
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32
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15437
AN XY:
74016
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3456
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at