chr9-121758976-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4BP6_ModerateBP7BS1BS2
The NM_001395010.1(DAB2IP):c.595C>A(p.Arg199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00203 in 1,612,870 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0086 ( 14 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 14 hom. )
Consequence
DAB2IP
NM_001395010.1 synonymous
NM_001395010.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.92
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.15).
BP6
?
Variant 9-121758976-C-A is Benign according to our data. Variant chr9-121758976-C-A is described in ClinVar as [Benign]. Clinvar id is 713727.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.92 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00856 (1304/152286) while in subpopulation AFR AF= 0.0256 (1063/41556). AF 95% confidence interval is 0.0243. There are 14 homozygotes in gnomad4. There are 672 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1294 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB2IP | NM_001395010.1 | c.595C>A | p.Arg199= | synonymous_variant | 5/16 | ENST00000408936.8 | |
DAB2IP | NM_032552.4 | c.511C>A | p.Arg171= | synonymous_variant | 5/17 | ||
DAB2IP | NM_138709.2 | c.223C>A | p.Arg75= | synonymous_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB2IP | ENST00000408936.8 | c.595C>A | p.Arg199= | synonymous_variant | 5/16 | 5 | NM_001395010.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00850 AC: 1294AN: 152168Hom.: 14 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1294
AN:
152168
Hom.:
Cov.:
33
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: 0.00317 AC: 788AN: 248220Hom.: 9 AF XY: 0.00276 AC XY: 370AN XY: 133924
GnomAD3 exomes
AF:
AC:
788
AN:
248220
Hom.:
AF XY:
AC XY:
370
AN XY:
133924
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: 0.00135 AC: 1975AN: 1460584Hom.: 14 Cov.: 31 AF XY: 0.00131 AC XY: 948AN XY: 726338
GnomAD4 exome
AF:
AC:
1975
AN:
1460584
Hom.:
Cov.:
31
AF XY:
AC XY:
948
AN XY:
726338
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: 0.00856 AC: 1304AN: 152286Hom.: 14 Cov.: 33 AF XY: 0.00903 AC XY: 672AN XY: 74452
GnomAD4 genome
?
AF:
AC:
1304
AN:
152286
Hom.:
Cov.:
33
AF XY:
AC XY:
672
AN XY:
74452
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:
Asia WGS
AF:
AC:
33
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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