6-15593088-G-GA
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_032122.5(DTNBP1):c.489-8_489-7insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,236,686 control chromosomes in the GnomAD database, including 2,611 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032122.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTNBP1 | NM_032122.5 | c.489-8_489-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000344537.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTNBP1 | ENST00000344537.10 | c.489-8_489-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032122.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.178 AC: 24111AN: 135696Hom.: 2288 Cov.: 28
GnomAD4 exome AF: 0.210 AC: 230914AN: 1100954Hom.: 326 Cov.: 0 AF XY: 0.209 AC XY: 114865AN XY: 548704
GnomAD4 genome AF: 0.178 AC: 24117AN: 135732Hom.: 2285 Cov.: 28 AF XY: 0.179 AC XY: 11698AN XY: 65400
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | - - |
Hermansky-Pudlak syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at