rs17203281
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001321075.3(DLG4):c.1167C>T(p.Ile389Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,613,368 control chromosomes in the GnomAD database, including 77,375 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001321075.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLG4 | ENST00000399506.9 | c.1167C>T | p.Ile389Ile | synonymous_variant | Exon 10 of 20 | 2 | NM_001321075.3 | ENSP00000382425.2 | ||
DLG4 | ENST00000648172.8 | c.1296C>T | p.Ile432Ile | synonymous_variant | Exon 12 of 22 | ENSP00000497806.3 | ||||
DLG4 | ENST00000648896.1 | c.1266C>T | p.Ile422Ile | synonymous_variant | Exon 10 of 20 | ENSP00000497546.1 | ||||
DLG4 | ENST00000649520.1 | c.987C>T | p.Ile329Ile | synonymous_variant | Exon 9 of 19 | ENSP00000497647.1 | ||||
DLG4 | ENST00000648263.1 | c.987C>T | p.Ile329Ile | synonymous_variant | Exon 8 of 14 | ENSP00000498035.1 | ||||
DLG4 | ENST00000491753.2 | n.1296C>T | non_coding_transcript_exon_variant | Exon 12 of 21 | 2 | ENSP00000467897.2 |
Frequencies
GnomAD3 genomes AF: 0.281 AC: 42701AN: 151992Hom.: 6380 Cov.: 32
GnomAD3 exomes AF: 0.283 AC: 70531AN: 249188Hom.: 10847 AF XY: 0.286 AC XY: 38690AN XY: 135178
GnomAD4 exome AF: 0.307 AC: 449018AN: 1461258Hom.: 70993 Cov.: 39 AF XY: 0.306 AC XY: 222099AN XY: 726908
GnomAD4 genome AF: 0.281 AC: 42707AN: 152110Hom.: 6382 Cov.: 32 AF XY: 0.281 AC XY: 20898AN XY: 74360
ClinVar
Submissions by phenotype
not provided Benign:2
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Intellectual developmental disorder 62 Benign:1
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DLG4-related disorder Benign:1
This variant is classified as 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