chr20-45410018-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001048225.4(DBNDD2):c.364G>T(p.Asp122Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000129 in 1,551,952 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D122A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001048225.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DBNDD2 | NM_001048225.4 | c.364G>T | p.Asp122Tyr | missense_variant | 3/3 | ENST00000372710.5 | |
SYS1-DBNDD2 | NR_003189.2 | n.752G>T | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBNDD2 | ENST00000372710.5 | c.364G>T | p.Asp122Tyr | missense_variant | 3/3 | 1 | NM_001048225.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000650 AC: 1AN: 153960Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81446
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1399846Hom.: 0 Cov.: 33 AF XY: 0.0000116 AC XY: 8AN XY: 690406
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.670G>T (p.D224Y) alteration is located in exon 3 (coding exon 3) of the DBNDD2 gene. This alteration results from a G to T substitution at nucleotide position 670, causing the aspartic acid (D) at amino acid position 224 to be replaced by a tyrosine (Y). 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