chr5-39381475-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001343.4(DAB2):c.1483G>A(p.Val495Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001343.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB2 | NM_001343.4 | c.1483G>A | p.Val495Met | missense_variant | 11/15 | ENST00000320816.11 | |
DAB2 | NM_001244871.2 | c.1420G>A | p.Val474Met | missense_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2 | ENST00000320816.11 | c.1483G>A | p.Val495Met | missense_variant | 11/15 | 1 | NM_001343.4 | P3 | |
DAB2 | ENST00000509337.5 | c.1420G>A | p.Val474Met | missense_variant | 9/13 | 1 | A1 | ||
DAB2 | ENST00000545653.5 | c.1420G>A | p.Val474Met | missense_variant | 10/14 | 5 | A1 | ||
DAB2 | ENST00000339788.10 | c.829G>A | p.Val277Met | missense_variant | 10/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250514Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135368
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461700Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727138
GnomAD4 genome AF: 0.000249 AC: 38AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1483G>A (p.V495M) alteration is located in exon 11 (coding exon 10) of the DAB2 gene. This alteration results from a G to A substitution at nucleotide position 1483, causing the valine (V) at amino acid position 495 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