rs73093419
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_173602.3(DIP2B):c.793G>A(p.Asp265Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00995 in 1,613,996 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0064 ( 6 hom., cov: 32)
Exomes 𝑓: 0.010 ( 99 hom. )
Consequence
DIP2B
NM_173602.3 missense
NM_173602.3 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 9.36
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=0.009075761).
BP6
?
Variant 12-50674626-G-A is Benign according to our data. Variant chr12-50674626-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 377262.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 980 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIP2B | NM_173602.3 | c.793G>A | p.Asp265Asn | missense_variant | 6/38 | ENST00000301180.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIP2B | ENST00000301180.10 | c.793G>A | p.Asp265Asn | missense_variant | 6/38 | 5 | NM_173602.3 | P1 | |
DIP2B | ENST00000546719.1 | n.570G>A | non_coding_transcript_exon_variant | 5/7 | 1 | ||||
DIP2B | ENST00000549620.5 | n.949G>A | non_coding_transcript_exon_variant | 6/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00645 AC: 981AN: 152194Hom.: 6 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00605 AC: 1518AN: 251060Hom.: 7 AF XY: 0.00578 AC XY: 785AN XY: 135698
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GnomAD4 exome AF: 0.0103 AC: 15075AN: 1461684Hom.: 99 Cov.: 31 AF XY: 0.00983 AC XY: 7145AN XY: 727122
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GnomAD4 genome ? AF: 0.00643 AC: 980AN: 152312Hom.: 6 Cov.: 32 AF XY: 0.00573 AC XY: 427AN XY: 74480
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89
ExAC
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752
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 15, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
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