chr20-45409956-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.302T>Cā(p.Leu101Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,551,700 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 (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 | UniProt |
---|---|---|---|---|---|---|---|
DBNDD2 | NM_001048225.4 | c.302T>C | p.Leu101Pro | missense_variant | 3/3 | ENST00000372710.5 | |
SYS1-DBNDD2 | NR_003189.2 | n.690T>C | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBNDD2 | ENST00000372710.5 | c.302T>C | p.Leu101Pro | missense_variant | 3/3 | 1 | NM_001048225.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000461 AC: 7AN: 151886Hom.: 0 AF XY: 0.0000372 AC XY: 3AN XY: 80576
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1399396Hom.: 0 Cov.: 34 AF XY: 0.0000116 AC XY: 8AN XY: 690202
GnomAD4 genome AF: 0.000144 AC: 22AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.608T>C (p.L203P) 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 608, causing the leucine (L) at amino acid position 203 to be replaced by a proline (P). 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