chr1-34904382-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001080418.3(DLGAP3):c.1002C>T(p.Thr334=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000514 in 1,613,732 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 3 hom. )
Consequence
DLGAP3
NM_001080418.3 synonymous
NM_001080418.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.01
Genes affected
DLGAP3 (HGNC:30368): (DLG associated protein 3) Predicted to enable PDZ domain binding activity; molecular adaptor activity; and scaffold protein binding activity. Predicted to be involved in protein-containing complex assembly and regulation of postsynaptic neurotransmitter receptor activity. Predicted to be located in synapse. Predicted to be part of postsynaptic density. Predicted to be active in several cellular components, including cholinergic synapse; glutamatergic synapse; and neuromuscular junction. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 1-34904382-G-A is Benign according to our data. Variant chr1-34904382-G-A is described in ClinVar as [Benign]. Clinvar id is 709546.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.01 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP3 | NM_001080418.3 | c.1002C>T | p.Thr334= | synonymous_variant | 3/12 | ENST00000373347.6 | |
DLGAP3 | XM_011541879.3 | c.1002C>T | p.Thr334= | synonymous_variant | 4/13 | ||
DLGAP3 | XM_047426631.1 | c.1002C>T | p.Thr334= | synonymous_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP3 | ENST00000373347.6 | c.1002C>T | p.Thr334= | synonymous_variant | 3/12 | 5 | NM_001080418.3 | P1 | |
DLGAP3 | ENST00000235180.4 | c.1002C>T | p.Thr334= | synonymous_variant | 1/10 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00293 AC: 446AN: 152226Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.000659 AC: 165AN: 250230Hom.: 1 AF XY: 0.000479 AC XY: 65AN XY: 135578
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GnomAD4 exome AF: 0.000262 AC: 383AN: 1461388Hom.: 3 Cov.: 32 AF XY: 0.000221 AC XY: 161AN XY: 727044
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GnomAD4 genome AF: 0.00293 AC: 446AN: 152344Hom.: 5 Cov.: 32 AF XY: 0.00286 AC XY: 213AN XY: 74502
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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 | Invitae | Oct 10, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at