chr6-170283029-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_005618.4(DLL1):c.2125G>A(p.Val709Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000638 in 1,614,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V709F) has been classified as Uncertain significance.
Frequency
Consequence
NM_005618.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLL1 | NM_005618.4 | c.2125G>A | p.Val709Ile | missense_variant | 10/11 | ENST00000366756.4 | |
DLL1 | XM_005266934.5 | c.1528G>A | p.Val510Ile | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLL1 | ENST00000366756.4 | c.2125G>A | p.Val709Ile | missense_variant | 10/11 | 1 | NM_005618.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251346Hom.: 1 AF XY: 0.000147 AC XY: 20AN XY: 135844
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461816Hom.: 0 Cov.: 34 AF XY: 0.0000770 AC XY: 56AN XY: 727192
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 04, 2023 | - - |
DLL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at