chr2-227889965-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178821.3(DAW1):c.223G>A(p.Gly75Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000876 in 1,598,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. G75D) has been classified as Uncertain significance.
Frequency
Consequence
NM_178821.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAW1 | NM_178821.3 | c.223G>A | p.Gly75Ser | missense_variant | 3/13 | ENST00000309931.3 | |
DAW1 | NM_001330004.2 | c.178G>A | p.Gly60Ser | missense_variant | 4/14 | ||
DAW1 | XM_047443536.1 | c.178G>A | p.Gly60Ser | missense_variant | 5/15 | ||
DAW1 | NR_138459.2 | n.282G>A | non_coding_transcript_exon_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAW1 | ENST00000309931.3 | c.223G>A | p.Gly75Ser | missense_variant | 3/13 | 1 | NM_178821.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000844 AC: 2AN: 236828Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128416
GnomAD4 exome AF: 0.00000760 AC: 11AN: 1446494Hom.: 0 Cov.: 30 AF XY: 0.00000834 AC XY: 6AN XY: 719450
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.223G>A (p.G75S) alteration is located in exon 3 (coding exon 3) of the DAW1 gene. This alteration results from a G to A substitution at nucleotide position 223, causing the glycine (G) at amino acid position 75 to be replaced by a serine (S). 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