1-46511199-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_172225.2(DMBX1):c.598G>C(p.Ala200Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00772 in 1,613,426 control chromosomes in the GnomAD database, including 869 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.041 ( 429 hom., cov: 33)
Exomes 𝑓: 0.0043 ( 440 hom. )
Consequence
DMBX1
NM_172225.2 missense
NM_172225.2 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 1.42
Genes affected
DMBX1 (HGNC:19026): (diencephalon/mesencephalon homeobox 1) This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015186667).
BP6
?
Variant 1-46511199-G-C is Benign according to our data. Variant chr1-46511199-G-C is described in ClinVar as [Benign]. Clinvar id is 3037813.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMBX1 | NM_172225.2 | c.598G>C | p.Ala200Pro | missense_variant | 5/6 | ENST00000360032.4 | |
DMBX1 | NM_001387776.1 | c.613G>C | p.Ala205Pro | missense_variant | 4/5 | ||
DMBX1 | NM_147192.4 | c.613G>C | p.Ala205Pro | missense_variant | 5/6 | ||
DMBX1 | NM_001387775.1 | c.598G>C | p.Ala200Pro | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMBX1 | ENST00000360032.4 | c.598G>C | p.Ala200Pro | missense_variant | 5/6 | 1 | NM_172225.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0408 AC: 6213AN: 152176Hom.: 426 Cov.: 33
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GnomAD3 exomes AF: 0.0103 AC: 2509AN: 244398Hom.: 167 AF XY: 0.00764 AC XY: 1019AN XY: 133364
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GnomAD4 exome AF: 0.00426 AC: 6228AN: 1461132Hom.: 440 Cov.: 34 AF XY: 0.00363 AC XY: 2638AN XY: 726864
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GnomAD4 genome ? AF: 0.0408 AC: 6220AN: 152294Hom.: 429 Cov.: 33 AF XY: 0.0397 AC XY: 2956AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DMBX1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
D;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MPC
0.49
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at