rs559479

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006496.4(GNAI3):​c.*3592T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,934 control chromosomes in the GnomAD database, including 15,655 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 0.42 ( 15655 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

GNAI3
NM_006496.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.429
Variant links:
Genes affected
GNAI3 (HGNC:4387): (G protein subunit alpha i3) Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling pathways. G proteins are composed of 3 units: alpha, beta and gamma. This gene encodes an alpha subunit and belongs to the G-alpha family. Mutation in this gene, resulting in a gly40-to-arg substitution, is associated with auriculocondylar syndrome, and shown to affect downstream targets in the G protein-coupled endothelin receptor pathway. [provided by RefSeq, Jun 2012]

Genome browser will be placed here

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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNAI3NM_006496.4 linkc.*3592T>A 3_prime_UTR_variant Exon 9 of 9 ENST00000369851.7 NP_006487.1 P08754

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNAI3ENST00000369851.7 linkc.*3592T>A 3_prime_UTR_variant Exon 9 of 9 1 NM_006496.4 ENSP00000358867.4 P08754

Frequencies

GnomAD3 genomes
AF:
0.419
AC:
63626
AN:
151816
Hom.:
15630
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.689
Gnomad AMI
AF:
0.399
Gnomad AMR
AF:
0.309
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.358
Gnomad SAS
AF:
0.484
Gnomad FIN
AF:
0.278
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.308
Gnomad OTH
AF:
0.383
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
Gnomad4 AFR exome
AC:
0
AN:
0
Gnomad4 AMR exome
AC:
0
AN:
0
Gnomad4 ASJ exome
AC:
0
AN:
0
Gnomad4 EAS exome
AC:
0
AN:
0
Gnomad4 SAS exome
AC:
0
AN:
0
Gnomad4 FIN exome
AC:
0
AN:
0
Gnomad4 NFE exome
AC:
0
AN:
0
Gnomad4 Remaining exome
AC:
0
AN:
0
GnomAD4 genome
AF:
0.419
AC:
63701
AN:
151934
Hom.:
15655
Cov.:
31
AF XY:
0.415
AC XY:
30848
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.689
AC:
0.688922
AN:
0.688922
Gnomad4 AMR
AF:
0.309
AC:
0.308841
AN:
0.308841
Gnomad4 ASJ
AF:
0.343
AC:
0.342561
AN:
0.342561
Gnomad4 EAS
AF:
0.358
AC:
0.358163
AN:
0.358163
Gnomad4 SAS
AF:
0.483
AC:
0.483195
AN:
0.483195
Gnomad4 FIN
AF:
0.278
AC:
0.277693
AN:
0.277693
Gnomad4 NFE
AF:
0.308
AC:
0.307575
AN:
0.307575
Gnomad4 OTH
AF:
0.382
AC:
0.381905
AN:
0.381905
Heterozygous variant carriers
0
1636
3272
4909
6545
8181
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
574
1148
1722
2296
2870
<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:
0.374
Hom.:
1485
Bravo
AF:
0.430
Asia WGS
AF:
0.430
AC:
1493
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.2
DANN
Benign
0.83

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: rs559479; hg19: chr1-110138536; API