20-45406590-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000372720.7(DBNDD2):c.139C>T(p.Arg47Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000184 in 1,304,082 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYS1-DBNDD2 | NR_003189.2 | n.381-1870C>T | intron_variant, non_coding_transcript_variant | ||||
LOC107985404 | XR_007067608.1 | n.142-158G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBNDD2 | ENST00000372720.7 | c.139C>T | p.Arg47Cys | missense_variant | 1/4 | 1 | |||
DBNDD2 | ENST00000372717.5 | c.-151C>T | 5_prime_UTR_variant | 1/4 | 5 | ||||
DBNDD2 | ENST00000357275.6 | c.-9+335C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000184 AC: 24AN: 1304082Hom.: 0 Cov.: 31 AF XY: 0.0000157 AC XY: 10AN XY: 636670
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.139C>T (p.R47C) alteration is located in exon 1 (coding exon 1) of the DBNDD2 gene. This alteration results from a C to T substitution at nucleotide position 139, causing the arginine (R) at amino acid position 47 to be replaced by a cysteine (C). 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