NM_004297.4:c.310-26809C>T

Variant names:

• chr9-77461331-G-A
• rs3780293
• NM_004297.4:c.310-26809C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004297.4(GNA14):​c.310-26809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,184 control chromosomes in the GnomAD database, including 21,532 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 0.46 (21532 hom., cov: 33)
• Consequence: GNA14 NM_004297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 14 publications found

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]

GNA14-AS1 (HGNC:50451): (GNA14 antisense RNA 1)

ENSG00000295843 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004297.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA14	NM_004297.4	MANE Select	c.310-26809C>T		intron	N/A	NP_004288.1	O95837
	GNA14-AS1	NR_121184.1		n.261+4809G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA14	ENST00000341700.7	TSL:1 MANE Select	c.310-26809C>T		intron	N/A	ENSP00000365807.4	O95837
	GNA14-AS1	ENST00000439145.1	TSL:1	n.228+4809G>A		intron	N/A
	ENSG00000295843	ENST00000732943.1		n.49-7244G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70638 AN: 152066 Hom.: 21471 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.439

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.465 AC: 70746 AN: 152184 Hom.: 21532 Cov.: 33 AF XY: 0.456 AC XY: 33917 AN XY: 74378

African (AFR) AF: 0.871 AC: 36176 AN: 41552

American (AMR) AF: 0.316 AC: 4836 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3470

East Asian (EAS) AF: 0.139 AC: 720 AN: 5182

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4812

European-Finnish (FIN) AF: 0.280 AC: 2958 AN: 10578

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22122 AN: 67982

Other (OTH) AF: 0.436 AC: 919 AN: 2106

Alfa AF: 0.372 Hom.: 41685

Bravo AF: 0.487

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3780293; hg19: chr9-80076247;