chr7-80011397-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000649225.1(GNAI1):c.-337+54331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,150 control chromosomes in the GnomAD database, including 1,692 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 1692 hom., cov: 32)
Consequence
GNAI1
ENST00000649225.1 intron
ENST00000649225.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.330
Publications
2 publications found
Genes affected
GNAI1 (HGNC:4384): (G protein subunit alpha i1) Guanine nucleotide binding proteins are heterotrimeric signal-transducing molecules consisting of alpha, beta, and gamma subunits. The alpha subunit binds guanine nucleotide, can hydrolyze GTP, and can interact with other proteins. The protein encoded by this gene represents the alpha subunit of an inhibitory complex. The encoded protein is part of a complex that responds to beta-adrenergic signals by inhibiting adenylate cyclase. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
GNAI1 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- neurodevelopmental disorder with hypotonia, impaired speech, and behavioral abnormalitiesInheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Broad Center for Mendelian Genomics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.146 AC: 22232AN: 152032Hom.: 1688 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
22232
AN:
152032
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.146 AC: 22250AN: 152150Hom.: 1692 Cov.: 32 AF XY: 0.145 AC XY: 10785AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
22250
AN:
152150
Hom.:
Cov.:
32
AF XY:
AC XY:
10785
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
5712
AN:
41518
American (AMR)
AF:
AC:
1742
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
326
AN:
3466
East Asian (EAS)
AF:
AC:
811
AN:
5184
South Asian (SAS)
AF:
AC:
364
AN:
4816
European-Finnish (FIN)
AF:
AC:
1666
AN:
10592
Middle Eastern (MID)
AF:
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11177
AN:
67982
Other (OTH)
AF:
AC:
309
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
954
1907
2861
3814
4768
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
246
492
738
984
1230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
390
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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