9-121737701-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001395010.1(DAB2IP):c.363-19312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 985,438 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 12 hom. )
Consequence
DAB2IP
NM_001395010.1 intron
NM_001395010.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-121737701-G-A is Benign according to our data. Variant chr9-121737701-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2659479.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 479 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB2IP | NM_001395010.1 | c.363-19312G>A | intron_variant | ENST00000408936.8 | |||
DAB2IP | NM_032552.4 | c.279-19312G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2IP | ENST00000408936.8 | c.363-19312G>A | intron_variant | 5 | NM_001395010.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00315 AC: 479AN: 152210Hom.: 1 Cov.: 33
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GnomAD4 exome AF: 0.00338 AC: 2820AN: 833110Hom.: 12 Cov.: 29 AF XY: 0.00343 AC XY: 1321AN XY: 384714
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GnomAD4 genome AF: 0.00314 AC: 479AN: 152328Hom.: 1 Cov.: 33 AF XY: 0.00305 AC XY: 227AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | DAB2IP: BP4, BP7 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at