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GeneBe

rs6967965

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000649225.1(GNAI1):​c.-433-20208T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,156 control chromosomes in the GnomAD database, including 2,705 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 0.18 ( 2705 hom., cov: 32)

Consequence

GNAI1
ENST00000649225.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.410
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GNAI1ENST00000649225.1 linkuse as main transcriptc.-433-20208T>C intron_variant P1P63096-1
GNAI1ENST00000650351.1 linkuse as main transcriptn.383-20208T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.179
AC:
27186
AN:
152038
Hom.:
2698
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.239
Gnomad AMI
AF:
0.158
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.0431
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.188
Gnomad OTH
AF:
0.159
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.179
AC:
27223
AN:
152156
Hom.:
2705
Cov.:
32
AF XY:
0.174
AC XY:
12933
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.240
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.000772
Gnomad4 SAS
AF:
0.0433
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.188
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.177
Hom.:
1197
Bravo
AF:
0.177
Asia WGS
AF:
0.0420
AC:
149
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
6.4
DANN
Benign
0.49

Splicing

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: rs6967965; hg19: chr7-79566078; API