20-45409935-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001048225.4(DBNDD2):āc.281T>Cā(p.Met94Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,551,604 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 (ā ).
Frequency
Consequence
NM_001048225.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DBNDD2 | NM_001048225.4 | c.281T>C | p.Met94Thr | missense_variant | 3/3 | ENST00000372710.5 | NP_001041690.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DBNDD2 | ENST00000372710.5 | c.281T>C | p.Met94Thr | missense_variant | 3/3 | 1 | NM_001048225.4 | ENSP00000361795.4 | ||
SYS1-DBNDD2 | ENST00000458187.5 | n.*287T>C | non_coding_transcript_exon_variant | 6/6 | 5 | ENSP00000457768.1 | ||||
SYS1-DBNDD2 | ENST00000458187.5 | n.*287T>C | 3_prime_UTR_variant | 6/6 | 5 | ENSP00000457768.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000198 AC: 3AN: 151694Hom.: 0 AF XY: 0.0000248 AC XY: 2AN XY: 80484
GnomAD4 exome AF: 0.00000929 AC: 13AN: 1399362Hom.: 0 Cov.: 34 AF XY: 0.0000130 AC XY: 9AN XY: 690194
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.587T>C (p.M196T) alteration is located in exon 3 (coding exon 3) of the DBNDD2 gene. This alteration results from a T to C substitution at nucleotide position 587, causing the methionine (M) at amino acid position 196 to be replaced by a threonine (T). 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