rs11145462

Variant summary

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

The NM_004297.4(GNA14):​c.309+875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,842 control chromosomes in the GnomAD database, including 18,075 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 0.48 ( 18075 hom., cov: 31)

Consequence

GNA14
NM_004297.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23
Variant links:
Genes affected
GNA14 (HGNC:4382): (G protein subunit alpha 14) This gene encodes a member of the guanine nucleotide-binding, or G protein family. G proteins are heterotrimers consisting of alpha, beta and gamma subunits. The encoded protein is a member of the alpha family of G proteins, more specifically the alpha q subfamily of G proteins. The encoded protein may play a role in pertussis-toxin resistant activation of phospholipase C-beta and its downstream effectors.[provided by RefSeq, Feb 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GNA14NM_004297.4 linkuse as main transcriptc.309+875C>T intron_variant ENST00000341700.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GNA14ENST00000341700.7 linkuse as main transcriptc.309+875C>T intron_variant 1 NM_004297.4 P1

Frequencies

GnomAD3 genomes
AF:
0.479
AC:
72694
AN:
151724
Hom.:
18076
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.344
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.584
Gnomad ASJ
AF:
0.449
Gnomad EAS
AF:
0.462
Gnomad SAS
AF:
0.506
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.455
Gnomad NFE
AF:
0.530
Gnomad OTH
AF:
0.499
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.479
AC:
72721
AN:
151842
Hom.:
18075
Cov.:
31
AF XY:
0.481
AC XY:
35708
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.344
Gnomad4 AMR
AF:
0.584
Gnomad4 ASJ
AF:
0.449
Gnomad4 EAS
AF:
0.462
Gnomad4 SAS
AF:
0.506
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.530
Gnomad4 OTH
AF:
0.496
Alfa
AF:
0.518
Hom.:
41746
Bravo
AF:
0.477
Asia WGS
AF:
0.442
AC:
1536
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.6
DANN
Benign
0.84

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: rs11145462; hg19: chr9-80143110; API