9-121678780-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001395010.1(DAB2IP):c.227C>T(p.Thr76Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000909 in 1,583,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000085 ( 0 hom. )
Consequence
DAB2IP
NM_001395010.1 missense, splice_region
NM_001395010.1 missense, splice_region
Scores
2
7
8
Splicing: ADA: 0.9301
2
Clinical Significance
Conservation
PhyloP100: 4.62
Genes affected
DAB2IP (HGNC:17294): (DAB2 interacting protein) DAB2IP is a Ras (MIM 190020) GTPase-activating protein (GAP) that acts as a tumor suppressor. The DAB2IP gene is inactivated by methylation in prostate and breast cancers (Yano et al., 2005 [PubMed 15386433]).[supplied by OMIM, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.16563725).
BS2
?
High AC in GnomAd at 22 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB2IP | NM_001395010.1 | c.227C>T | p.Thr76Met | missense_variant, splice_region_variant | 2/16 | ENST00000408936.8 | |
DAB2IP | NM_032552.4 | c.143C>T | p.Thr48Met | missense_variant, splice_region_variant | 2/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2IP | ENST00000408936.8 | c.227C>T | p.Thr76Met | missense_variant, splice_region_variant | 2/16 | 5 | NM_001395010.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152236Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000852 AC: 18AN: 211290Hom.: 0 AF XY: 0.0000601 AC XY: 7AN XY: 116406
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GnomAD4 exome AF: 0.0000853 AC: 122AN: 1430988Hom.: 0 Cov.: 30 AF XY: 0.0000846 AC XY: 60AN XY: 709406
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GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74502
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.143C>T (p.T48M) alteration is located in exon 2 (coding exon 2) of the DAB2IP gene. This alteration results from a C to T substitution at nucleotide position 143, causing the threonine (T) at amino acid position 48 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;.;N
REVEL
Benign
Sift
Uncertain
D;D;.;D
Sift4G
Uncertain
D;T;.;D
Vest4
0.66, 0.69
MVP
MPC
1.5
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at