rs202028496
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001371333.1(DIABLO):āc.8C>Gā(p.Ala3Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,603,470 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001371333.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIABLO | NM_001371333.1 | c.8C>G | p.Ala3Gly | missense_variant | 1/6 | ENST00000464942.7 | NP_001358262.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000762 AC: 116AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000767 AC: 175AN: 228220Hom.: 0 AF XY: 0.000776 AC XY: 97AN XY: 124990
GnomAD4 exome AF: 0.00104 AC: 1512AN: 1451118Hom.: 2 Cov.: 32 AF XY: 0.00101 AC XY: 730AN XY: 721152
GnomAD4 genome AF: 0.000761 AC: 116AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 22, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 03, 2017 | p.Ala3Gly in exon 2 of DIABLO: This variant is not expected to have clinical sig nificance because it has been identified in various populations with highest fre quencies in 0.16% (54/33120) of Latino chromosomes, 0.12% (12/9630) of Ashkenazi Jewish chromosomes, and 0.11% (107/113660) of European chromosomes by the Genom e Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs20202 8496). - |
DIABLO-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2024 | 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