chr4-143439755-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002039.4(GAB1):c.1196-47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,336,290 control chromosomes in the GnomAD database, including 608 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 91 hom., cov: 32)
Exomes 𝑓: 0.010 ( 517 hom. )
Consequence
GAB1
NM_002039.4 intron
NM_002039.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.577
Genes affected
GAB1 (HGNC:4066): (GRB2 associated binding protein 1) The protein encoded by this gene is a member of the IRS1-like multisubstrate docking protein family. It is an important mediator of branching tubulogenesis and plays a central role in cellular growth response, transformation and apoptosis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 4-143439755-G-A is Benign according to our data. Variant chr4-143439755-G-A is described in ClinVar as [Benign]. Clinvar id is 1278037.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAB1 | NM_002039.4 | c.1196-47G>A | intron_variant | ENST00000262994.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAB1 | ENST00000262994.9 | c.1196-47G>A | intron_variant | 1 | NM_002039.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0128 AC: 1954AN: 152176Hom.: 90 Cov.: 32
GnomAD3 genomes
AF:
AC:
1954
AN:
152176
Hom.:
Cov.:
32
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: 0.0243 AC: 5858AN: 240880Hom.: 424 AF XY: 0.0193 AC XY: 2505AN XY: 130124
GnomAD3 exomes
AF:
AC:
5858
AN:
240880
Hom.:
AF XY:
AC XY:
2505
AN XY:
130124
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: 0.0101 AC: 11949AN: 1183996Hom.: 517 Cov.: 16 AF XY: 0.00914 AC XY: 5505AN XY: 602544
GnomAD4 exome
AF:
AC:
11949
AN:
1183996
Hom.:
Cov.:
16
AF XY:
AC XY:
5505
AN XY:
602544
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: 0.0129 AC: 1960AN: 152294Hom.: 91 Cov.: 32 AF XY: 0.0142 AC XY: 1058AN XY: 74460
GnomAD4 genome
AF:
AC:
1960
AN:
152294
Hom.:
Cov.:
32
AF XY:
AC XY:
1058
AN XY:
74460
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:
20
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 | GeneDx | May 12, 2021 | - - |
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