9-121758898-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001395010.1(DAB2IP):c.517G>A(p.Val173Met) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395010.1 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
DAB2IP | NM_001395010.1 | c.517G>A | p.Val173Met | missense_variant, splice_region_variant | 5/16 | ENST00000408936.8 | |
DAB2IP | NM_032552.4 | c.433G>A | p.Val145Met | missense_variant, splice_region_variant | 5/17 | ||
DAB2IP | NM_138709.2 | c.145G>A | p.Val49Met | missense_variant, splice_region_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2IP | ENST00000408936.8 | c.517G>A | p.Val173Met | missense_variant, splice_region_variant | 5/16 | 5 | NM_001395010.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152188Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460636Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726366
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.433G>A (p.V145M) alteration is located in exon 5 (coding exon 5) of the DAB2IP gene. This alteration results from a G to A substitution at nucleotide position 433, causing the valine (V) at amino acid position 145 to be replaced by a methionine (M). 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