rs16953073
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378457.1(DMXL2):āc.2707A>Gā(p.Asn903Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000946 in 1,611,372 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N903N) has been classified as Likely benign.
Frequency
Consequence
NM_001378457.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMXL2 | NM_001378457.1 | c.2707A>G | p.Asn903Asp | missense_variant | 16/44 | ENST00000560891.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMXL2 | ENST00000560891.6 | c.2707A>G | p.Asn903Asp | missense_variant | 16/44 | 1 | NM_001378457.1 | A1 | |
DMXL2 | ENST00000543779.6 | c.2707A>G | p.Asn903Asp | missense_variant | 16/43 | 1 | P4 | ||
DMXL2 | ENST00000251076.9 | c.2707A>G | p.Asn903Asp | missense_variant | 16/43 | 1 | A1 | ||
DMXL2 | ENST00000449909.7 | c.2707A>G | p.Asn903Asp | missense_variant | 16/41 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00529 AC: 805AN: 152216Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00135 AC: 338AN: 250648Hom.: 2 AF XY: 0.00102 AC XY: 138AN XY: 135524
GnomAD4 exome AF: 0.000493 AC: 720AN: 1459038Hom.: 4 Cov.: 29 AF XY: 0.000435 AC XY: 316AN XY: 725968
GnomAD4 genome ? AF: 0.00528 AC: 804AN: 152334Hom.: 8 Cov.: 32 AF XY: 0.00470 AC XY: 350AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at