5-119118985-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001290321.3(DMXL1):c.914G>A(p.Arg305Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,611,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001290321.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DMXL1 | ENST00000539542.6 | c.914G>A | p.Arg305Gln | missense_variant | 8/44 | 1 | NM_001290321.3 | ENSP00000439479.1 | ||
DMXL1 | ENST00000311085.8 | c.914G>A | p.Arg305Gln | missense_variant | 8/43 | 1 | ENSP00000309690.8 | |||
DMXL1 | ENST00000503802.5 | c.914G>A | p.Arg305Gln | missense_variant | 9/13 | 1 | ENSP00000427692.1 | |||
DMXL1 | ENST00000514151.1 | n.416-1986G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459058Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 725802
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.914G>A (p.R305Q) alteration is located in exon 8 (coding exon 8) of the DMXL1 gene. This alteration results from a G to A substitution at nucleotide position 914, causing the arginine (R) at amino acid position 305 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