rs1319305420

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024043.4(DBNDD1):​c.73G>C​(p.Gly25Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G25S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

DBNDD1
NM_024043.4 missense

Scores

2
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.781
Variant links:
Genes affected
DBNDD1 (HGNC:28455): (dysbindin domain containing 1) Predicted to be involved in negative regulation of protein kinase activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06788775).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DBNDD1NM_001042610.3 linkc.32-545G>C intron_variant Intron 1 of 3 ENST00000002501.11 NP_001036075.1 Q9H9R9-1
DBNDD1NM_024043.4 linkc.73G>C p.Gly25Arg missense_variant Exon 1 of 4 NP_076948.2 Q9H9R9-2
DBNDD1NM_001288708.2 linkc.32-545G>C intron_variant Intron 2 of 4 NP_001275637.1 Q9H9R9
DBNDD1NM_001288709.2 linkc.-215-545G>C intron_variant Intron 1 of 3 NP_001275638.2 Q9H9R9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DBNDD1ENST00000002501.11 linkc.32-545G>C intron_variant Intron 1 of 3 2 NM_001042610.3 ENSP00000002501.6 Q9H9R9-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
0.67
DANN
Benign
0.70
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.015
N
LIST_S2
Benign
0.52
T
M_CAP
Benign
0.0020
T
MetaRNN
Benign
0.068
T
MetaSVM
Benign
-1.1
T
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-0.16
N
REVEL
Benign
0.013
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.0010
B
Vest4
0.15
MutPred
0.42
Gain of MoRF binding (P = 0.0351);
MVP
0.048
MPC
0.13
ClinPred
0.23
T
GERP RS
-2.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1319305420; hg19: chr16-90076383; API