20-45406566-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000372720.7(DBNDD2):c.115C>G(p.His39Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,489,658 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000372720.7 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 |
---|---|---|---|---|---|---|---|
SYS1-DBNDD2 | NR_003189.2 | n.381-1894C>G | intron_variant, non_coding_transcript_variant | ||||
LOC107985404 | XR_007067608.1 | n.142-134G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBNDD2 | ENST00000372720.7 | c.115C>G | p.His39Asp | missense_variant | 1/4 | 1 | |||
DBNDD2 | ENST00000357275.6 | c.-9+311C>G | intron_variant | 5 | P1 | ||||
DBNDD2 | ENST00000372722.7 | c.-9+356C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000605 AC: 92AN: 152132Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000361 AC: 31AN: 85782Hom.: 0 AF XY: 0.000294 AC XY: 14AN XY: 47636
GnomAD4 exome AF: 0.0000501 AC: 67AN: 1337526Hom.: 0 Cov.: 31 AF XY: 0.0000518 AC XY: 34AN XY: 656700
GnomAD4 genome ? AF: 0.000605 AC: 92AN: 152132Hom.: 1 Cov.: 33 AF XY: 0.000834 AC XY: 62AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.115C>G (p.H39D) alteration is located in exon 1 (coding exon 1) of the DBNDD2 gene. This alteration results from a C to G substitution at nucleotide position 115, causing the histidine (H) at amino acid position 39 to be replaced by an aspartic acid (D). 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