chr20-36432412-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001365621.2(DLGAP4):c.695G>A(p.Arg232His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,613,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R232C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365621.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP4 | NM_001365621.2 | c.695G>A | p.Arg232His | missense_variant | 3/13 | ENST00000339266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP4 | ENST00000339266.10 | c.695G>A | p.Arg232His | missense_variant | 3/13 | 5 | NM_001365621.2 | ||
DLGAP4 | ENST00000373913.7 | c.695G>A | p.Arg232His | missense_variant | 3/13 | 1 | |||
DLGAP4 | ENST00000373907.6 | c.695G>A | p.Arg232His | missense_variant | 2/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 249876Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135522
GnomAD4 exome AF: 0.000125 AC: 183AN: 1461356Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 727008
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.695G>A (p.R232H) alteration is located in exon 2 (coding exon 1) of the DLGAP4 gene. This alteration results from a G to A substitution at nucleotide position 695, causing the arginine (R) at amino acid position 232 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at