GeneBe

X-154706415-CAAAA-CAAAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001081573.3(GAB3):​c.1069+5809_1069+5813dupTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000011 ( 0 hom., 0 hem., cov: 0)

Consequence

GAB3
NM_001081573.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193

Publications

1 publications found
Variant links:
Genes affected
GAB3 (HGNC:17515): (GRB2 associated binding protein 3) This gene is a member of the GRB2-associated binding protein gene family. These proteins are scaffolding/docking proteins that are involved in several growth factor and cytokine signaling pathways, and they contain a pleckstrin homology domain, and bind SHP2 tyrosine phosphatase and GRB2 adapter protein. The protein encoded by this gene facilitates macrophage differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GAB3NM_001081573.3 linkc.1069+5809_1069+5813dupTTTTT intron_variant Intron 4 of 9 ENST00000424127.3 NP_001075042.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GAB3ENST00000424127.3 linkc.1069+5813_1069+5814insTTTTT intron_variant Intron 4 of 9 1 NM_001081573.3 ENSP00000399588.2
GAB3ENST00000369575.7 linkc.1066+5813_1066+5814insTTTTT intron_variant Intron 4 of 9 1 ENSP00000358588.3
GAB3ENST00000496390.5 linkn.617-6357_617-6356insTTTTT intron_variant Intron 3 of 8 1
GAB3ENST00000369568.8 linkc.1069+5813_1069+5814insTTTTT intron_variant Intron 4 of 8 2 ENSP00000358581.4

Frequencies

GnomAD3 genomes
AF:
0.0000107
AC:
1
AN:
93554
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000211
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000107
AC:
1
AN:
93554
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
20598
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
24733
American (AMR)
AF:
0.00
AC:
0
AN:
8550
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2386
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3045
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2014
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3434
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
205
European-Non Finnish (NFE)
AF:
0.0000211
AC:
1
AN:
47349
Other (OTH)
AF:
0.00
AC:
0
AN:
1235
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.19

Splicing

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

Publications

Other links and lift over

dbSNP: rs35975601; hg19: chrX-153934690; API