rs11145462

chr9-77528194-G-Achr9-77528194-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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]

ACMG classification

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
GNA14	NM_004297.4	c.309+875C>T		intron_variant		ENST00000341700.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA14	ENST00000341700.7	c.309+875C>T		intron_variant		1	NM_004297.4	P1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72694 AN: 151724 Hom.: 18076 Cov.: 31

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

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

Other links and lift over

dbSNP: rs11145462; hg19: chr9-80143110;