rs3780293

Positions:

• chr9-77461331-G-A
• chr9-77461331-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.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

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)

LOC124902185 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNA14	NM_004297.4	c.310-26809C>T		intron_variant		ENST00000341700.7
GNA14-AS1	NR_121184.1	n.261+4809G>A		intron_variant, non_coding_transcript_variant
LOC124902185	XR_007061598.1	n.83+4166G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA14	ENST00000341700.7	c.310-26809C>T		intron_variant		1	NM_004297.4	P1
GNA14-AS1	ENST00000439145.1	n.228+4809G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.436

Alfa AF: 0.342 Hom.: 20484

Bravo AF: 0.487

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.60

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: rs3780293; hg19: chr9-80076247;