rs17860720
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005618.4(DLL1):c.*184C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00701 in 937,340 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 1 hom., cov: 34)
Exomes 𝑓: 0.0073 ( 47 hom. )
Consequence
DLL1
NM_005618.4 3_prime_UTR
NM_005618.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.413
Genes affected
DLL1 (HGNC:2908): (delta like canonical Notch ligand 1) DLL1 is a human homolog of the Notch Delta ligand and is a member of the delta/serrate/jagged family. It plays a role in mediating cell fate decisions during hematopoiesis. It may play a role in cell-to-cell communication. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 6-170282690-G-A is Benign according to our data. Variant chr6-170282690-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1254894.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00552 (841/152388) while in subpopulation NFE AF= 0.00775 (527/68038). AF 95% confidence interval is 0.0072. There are 1 homozygotes in gnomad4. There are 414 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 841 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLL1 | NM_005618.4 | c.*184C>T | 3_prime_UTR_variant | 11/11 | ENST00000366756.4 | ||
DLL1 | XM_005266934.5 | c.*184C>T | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLL1 | ENST00000366756.4 | c.*184C>T | 3_prime_UTR_variant | 11/11 | 1 | NM_005618.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00553 AC: 842AN: 152270Hom.: 1 Cov.: 34
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GnomAD4 exome AF: 0.00729 AC: 5726AN: 784952Hom.: 47 Cov.: 11 AF XY: 0.00715 AC XY: 2922AN XY: 408398
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GnomAD4 genome ? AF: 0.00552 AC: 841AN: 152388Hom.: 1 Cov.: 34 AF XY: 0.00556 AC XY: 414AN XY: 74516
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2021 | - - |
Computational 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