rs117722674
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_173602.3(DIP2B):āc.1060T>Cā(p.Ser354Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00168 in 1,614,212 control chromosomes in the GnomAD database, including 7 homozygotes. 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 Likely benign (ā ā ).
Frequency
Genomes: š 0.0011 ( 0 hom., cov: 31)
Exomes š: 0.0017 ( 7 hom. )
Consequence
DIP2B
NM_173602.3 missense
NM_173602.3 missense
Scores
19
Clinical Significance
Conservation
PhyloP100: 4.10
Genes affected
DIP2B (HGNC:29284): (disco interacting protein 2 homolog B) This gene encodes a member of the disco-interacting protein homolog 2 protein family. The encoded protein contains a binding site for the transcriptional regulator DNA methyltransferase 1 associated protein 1 as well as AMP-binding sites. The presence of these sites suggests that the encoded protein may participate in DNA methylation. This gene is located near a folate-sensitive fragile site, and CGG-repeat expansion in the promoter of this gene which affects transcription has been detected in individuals containing this fragile site on chromosome 12. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, DIP2B
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009845793).
BP6
?
Variant 12-50678822-T-C is Benign according to our data. Variant chr12-50678822-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 445445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-50678822-T-C is described in Lovd as [Likely_benign].
BS2
?
High AC in GnomAd4 at 169 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIP2B | NM_173602.3 | c.1060T>C | p.Ser354Pro | missense_variant | 8/38 | ENST00000301180.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIP2B | ENST00000301180.10 | c.1060T>C | p.Ser354Pro | missense_variant | 8/38 | 5 | NM_173602.3 | P1 | |
DIP2B | ENST00000546719.1 | n.837T>C | non_coding_transcript_exon_variant | 7/7 | 1 | ||||
DIP2B | ENST00000549620.5 | n.1216T>C | non_coding_transcript_exon_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00111 AC: 169AN: 152214Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000871 AC: 219AN: 251424Hom.: 0 AF XY: 0.000912 AC XY: 124AN XY: 135894
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GnomAD4 exome AF: 0.00174 AC: 2545AN: 1461880Hom.: 7 Cov.: 30 AF XY: 0.00174 AC XY: 1266AN XY: 727244
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GnomAD4 genome ? AF: 0.00111 AC: 169AN: 152332Hom.: 0 Cov.: 31 AF XY: 0.000926 AC XY: 69AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 21, 2017 | - - |
DIP2B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2023 | This variant is classified as likely 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
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
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