chr8-737814-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001346810.2(DLGAP2):c.7G>T(p.Ala3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00993 in 379,658 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 14 hom., cov: 33)
Exomes 𝑓: 0.011 ( 27 hom. )
Consequence
DLGAP2
NM_001346810.2 missense
NM_001346810.2 missense
Scores
6
Clinical Significance
Conservation
PhyloP100: 1.27
Genes affected
DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]
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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 (MetaRNN=0.004456252).
BP6
?
Variant 8-737814-G-T is Benign according to our data. Variant chr8-737814-G-T is described in ClinVar as [Benign]. Clinvar id is 3039242.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00888 (1345/151410) while in subpopulation SAS AF= 0.0321 (155/4834). AF 95% confidence interval is 0.0279. There are 14 homozygotes in gnomad4. There are 643 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP2 | NM_001346810.2 | c.7G>T | p.Ala3Ser | missense_variant | 1/15 | ENST00000637795.2 | |
DLGAP2 | NR_073397.2 | n.187G>T | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP2 | ENST00000637795.2 | c.7G>T | p.Ala3Ser | missense_variant | 1/15 | 5 | NM_001346810.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00888 AC: 1344AN: 151302Hom.: 14 Cov.: 33
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GnomAD4 exome AF: 0.0106 AC: 2425AN: 228248Hom.: 27 Cov.: 0 AF XY: 0.0110 AC XY: 1277AN XY: 116330
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GnomAD4 genome ? AF: 0.00888 AC: 1345AN: 151410Hom.: 14 Cov.: 33 AF XY: 0.00869 AC XY: 643AN XY: 73980
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DLGAP2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 18, 2019 | 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
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
GERP RS
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at