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GeneBe

9-121699387-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

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0450
Variant links:
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 -17 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.045 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 461 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DAB2IPNM_001395010.1 linkuse as main transcriptc.291C>T p.Asp97= synonymous_variant 3/16 ENST00000408936.8
DAB2IPNM_032552.4 linkuse as main transcriptc.207C>T p.Asp69= synonymous_variant 3/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DAB2IPENST00000408936.8 linkuse as main transcriptc.291C>T p.Asp97= synonymous_variant 3/165 NM_001395010.1 A1Q5VWQ8-1
DAB2IPENST00000259371.7 linkuse as main transcriptc.207C>T p.Asp69= synonymous_variant 3/175 Q5VWQ8-5
DAB2IPENST00000436835.6 linkuse as main transcriptc.144+20606C>T intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00308
AC:
461
AN:
149592
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000681
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00239
Gnomad ASJ
AF:
0.0134
Gnomad EAS
AF:
0.000196
Gnomad SAS
AF:
0.00333
Gnomad FIN
AF:
0.000922
Gnomad MID
AF:
0.00321
Gnomad NFE
AF:
0.00476
Gnomad OTH
AF:
0.00243
GnomAD3 exomes
AF:
0.00328
AC:
593
AN:
180762
Hom.:
1
AF XY:
0.00323
AC XY:
331
AN XY:
102438
show subpopulations
Gnomad AFR exome
AF:
0.000243
Gnomad AMR exome
AF:
0.000605
Gnomad ASJ exome
AF:
0.0123
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00324
Gnomad FIN exome
AF:
0.00218
Gnomad NFE exome
AF:
0.00416
Gnomad OTH exome
AF:
0.00385
GnomAD4 exome
AF:
0.00345
AC:
4593
AN:
1330736
Hom.:
19
Cov.:
33
AF XY:
0.00346
AC XY:
2288
AN XY:
661960
show subpopulations
Gnomad4 AFR exome
AF:
0.000405
Gnomad4 AMR exome
AF:
0.00107
Gnomad4 ASJ exome
AF:
0.0138
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00340
Gnomad4 FIN exome
AF:
0.00252
Gnomad4 NFE exome
AF:
0.00356
Gnomad4 OTH exome
AF:
0.00332
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00309
AC:
462
AN:
149694
Hom.:
1
Cov.:
31
AF XY:
0.00300
AC XY:
219
AN XY:
73096
show subpopulations
Gnomad4 AFR
AF:
0.000679
Gnomad4 AMR
AF:
0.00238
Gnomad4 ASJ
AF:
0.0134
Gnomad4 EAS
AF:
0.000197
Gnomad4 SAS
AF:
0.00354
Gnomad4 FIN
AF:
0.000922
Gnomad4 NFE
AF:
0.00476
Gnomad4 OTH
AF:
0.00240
Alfa
AF:
0.00442
Hom.:
0
Bravo
AF:
0.00283

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 submitterclinical testingInvitaeJul 06, 2018- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024DAB2IP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
Cadd
Benign
15
Dann
Benign
0.96

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200769141; hg19: chr9-124461666; API