17-7219739-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000399510.8(DLG4):c.-890T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000695 in 1,442,452 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 1 hom. )
Consequence
DLG4
ENST00000399510.8 5_prime_UTR
ENST00000399510.8 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.556
Genes affected
DLG4 (HGNC:2903): (discs large MAGUK scaffold protein 4) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. It heteromultimerizes with another MAGUK protein, DLG2, and is recruited into NMDA receptor and potassium channel clusters. These two MAGUK proteins may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
ACADVL (HGNC:92): (acyl-CoA dehydrogenase very long chain) The protein encoded by this gene is targeted to the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway. This acyl-Coenzyme A dehydrogenase is specific to long-chain and very-long-chain fatty acids. A deficiency in this gene product reduces myocardial fatty acid beta-oxidation and is associated with cardiomyopathy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 17-7219739-A-G is Benign according to our data. Variant chr17-7219739-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1214579.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 561 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG4 | NM_001321074.1 | c.-890T>C | 5_prime_UTR_variant | 1/22 | |||
DLG4 | NM_001365.4 | c.-890T>C | 5_prime_UTR_variant | 1/22 | |||
ACADVL | NM_001270447.2 | c.132-383A>G | intron_variant | ||||
DLG4 | NR_135527.1 | n.312T>C | non_coding_transcript_exon_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG4 | ENST00000399510.8 | c.-890T>C | 5_prime_UTR_variant | 1/22 | 1 | ||||
DLG4 | ENST00000648172.8 | c.-890T>C | 5_prime_UTR_variant | 1/22 | |||||
ACADVL | ENST00000543245.6 | c.132-383A>G | intron_variant | 2 | |||||
DLG4 | ENST00000491753.2 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00369 AC: 561AN: 152168Hom.: 3 Cov.: 32
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GnomAD4 exome AF: 0.000343 AC: 442AN: 1290166Hom.: 1 Cov.: 30 AF XY: 0.000281 AC XY: 176AN XY: 626964
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GnomAD4 genome ? AF: 0.00368 AC: 561AN: 152286Hom.: 3 Cov.: 32 AF XY: 0.00361 AC XY: 269AN XY: 74476
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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 | Oct 02, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at