chr17-7219637-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000399510.8(DLG4):c.-788C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0055 in 1,239,582 control chromosomes in the GnomAD database, including 316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 192 hom., cov: 32)
Exomes 𝑓: 0.0024 ( 124 hom. )
Consequence
DLG4
ENST00000399510.8 5_prime_UTR
ENST00000399510.8 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.37
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 17-7219637-G-A is Benign according to our data. Variant chr17-7219637-G-A is described in ClinVar as [Benign]. Clinvar id is 1246043.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG4 | NM_001321074.1 | c.-788C>T | 5_prime_UTR_variant | 1/22 | |||
DLG4 | NM_001365.4 | c.-788C>T | 5_prime_UTR_variant | 1/22 | |||
ACADVL | NM_001270447.2 | c.132-485G>A | intron_variant | ||||
DLG4 | NR_135527.1 | n.414C>T | non_coding_transcript_exon_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG4 | ENST00000399510.8 | c.-788C>T | 5_prime_UTR_variant | 1/22 | 1 | ||||
DLG4 | ENST00000648172.8 | c.-788C>T | 5_prime_UTR_variant | 1/22 | |||||
ACADVL | ENST00000543245.6 | c.132-485G>A | intron_variant | 2 | |||||
DLG4 | ENST00000491753.2 | c.-788C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0274 AC: 4163AN: 152054Hom.: 190 Cov.: 32
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GnomAD4 exome AF: 0.00243 AC: 2645AN: 1087410Hom.: 124 Cov.: 29 AF XY: 0.00223 AC XY: 1155AN XY: 519000
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GnomAD4 genome AF: 0.0274 AC: 4170AN: 152172Hom.: 192 Cov.: 32 AF XY: 0.0257 AC XY: 1912AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at