chr20-36432626-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001365621.2(DLGAP4):c.909C>A(p.His303Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,408 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP4 | NM_001365621.2 | c.909C>A | p.His303Gln | missense_variant | 3/13 | ENST00000339266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP4 | ENST00000339266.10 | c.909C>A | p.His303Gln | missense_variant | 3/13 | 5 | NM_001365621.2 | ||
DLGAP4 | ENST00000373913.7 | c.909C>A | p.His303Gln | missense_variant | 3/13 | 1 | |||
DLGAP4 | ENST00000373907.6 | c.909C>A | p.His303Gln | missense_variant | 2/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000286 AC: 7AN: 244762Hom.: 1 AF XY: 0.0000377 AC XY: 5AN XY: 132650
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460292Hom.: 1 Cov.: 35 AF XY: 0.0000262 AC XY: 19AN XY: 726228
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.909C>A (p.H303Q) alteration is located in exon 2 (coding exon 1) of the DLGAP4 gene. This alteration results from a C to A substitution at nucleotide position 909, causing the histidine (H) at amino acid position 303 to be replaced by a glutamine (Q). 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