chr9-121699387-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001395010.1(DAB2IP):c.291C>T(p.Asp97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 1,480,430 control chromosomes in the GnomAD database, including 20 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: 31)
Exomes 𝑓: 0.0035 ( 19 hom. )
Consequence
DAB2IP
NM_001395010.1 synonymous
NM_001395010.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0450
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 9-121699387-C-T is Benign according to our data. Variant chr9-121699387-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 781934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.045 with no splicing effect.
BS2
?
High AC in GnomAd at 461 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB2IP | NM_001395010.1 | c.291C>T | p.Asp97= | synonymous_variant | 3/16 | ENST00000408936.8 | |
DAB2IP | NM_032552.4 | c.207C>T | p.Asp69= | synonymous_variant | 3/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2IP | ENST00000408936.8 | c.291C>T | p.Asp97= | synonymous_variant | 3/16 | 5 | NM_001395010.1 | A1 | |
DAB2IP | ENST00000259371.7 | c.207C>T | p.Asp69= | synonymous_variant | 3/17 | 5 | |||
DAB2IP | ENST00000436835.6 | c.144+20606C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00308 AC: 461AN: 149592Hom.: 1 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
461
AN:
149592
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00328 AC: 593AN: 180762Hom.: 1 AF XY: 0.00323 AC XY: 331AN XY: 102438
GnomAD3 exomes
AF:
AC:
593
AN:
180762
Hom.:
AF XY:
AC XY:
331
AN XY:
102438
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00345 AC: 4593AN: 1330736Hom.: 19 Cov.: 33 AF XY: 0.00346 AC XY: 2288AN XY: 661960
GnomAD4 exome
AF:
AC:
4593
AN:
1330736
Hom.:
Cov.:
33
AF XY:
AC XY:
2288
AN XY:
661960
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00309 AC: 462AN: 149694Hom.: 1 Cov.: 31 AF XY: 0.00300 AC XY: 219AN XY: 73096
GnomAD4 genome
?
AF:
AC:
462
AN:
149694
Hom.:
Cov.:
31
AF XY:
AC XY:
219
AN XY:
73096
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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 | Jul 06, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | DAB2IP: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at