chr6-15524430-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_183040.2(DTNBP1):c.907G>A(p.Ala303Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,614,120 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_183040.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DTNBP1 | NM_032122.5 | c.811+96G>A | intron_variant | ENST00000344537.10 | NP_115498.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DTNBP1 | ENST00000344537.10 | c.811+96G>A | intron_variant | 1 | NM_032122.5 | ENSP00000341680.6 |
Frequencies
GnomAD3 genomes AF: 0.00409 AC: 622AN: 152156Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00340 AC: 854AN: 251472Hom.: 5 AF XY: 0.00352 AC XY: 479AN XY: 135906
GnomAD4 exome AF: 0.00553 AC: 8079AN: 1461846Hom.: 27 Cov.: 34 AF XY: 0.00538 AC XY: 3913AN XY: 727210
GnomAD4 genome AF: 0.00408 AC: 622AN: 152274Hom.: 1 Cov.: 33 AF XY: 0.00430 AC XY: 320AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | DTNBP1: BP4, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Ala303Thr in exon 9A of DTNBP1: This variant is not expected to have clinical si gnificance because it has been identified in 0.6% (49/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs16876569). - |
DTNBP1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 02, 2020 | 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