rs1122838

Positions:

• chr9-77648184-G-A
• chr9-77648184-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.-391C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 295,476 control chromosomes in the GnomAD database, including 5,613 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 0.20 (3318 hom., cov: 33)
  • Exomes 𝑓: 0.17 (2295 hom.)
• Consequence: GNA14 NM_004297.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNA14	NM_004297.4	c.-391C>T		5_prime_UTR_variant	1/7	ENST00000341700.7	NP_004288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNA14	ENST00000341700.7	c.-391C>T		5_prime_UTR_variant	1/7	1	NM_004297.4	ENSP00000365807.4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30101 AN: 152028 Hom.: 3303 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.167 AC: 23873 AN: 143330 Hom.: 2295 Cov.: 0 AF XY: 0.174 AC XY: 13269 AN XY: 76442

Gnomad4 AFR exome AF: 0.270

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.232

Gnomad4 SAS exome AF: 0.249

Gnomad4 FIN exome AF: 0.183

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.198 AC: 30150 AN: 152146 Hom.: 3318 Cov.: 33 AF XY: 0.201 AC XY: 14952 AN XY: 74368

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.222

Alfa AF: 0.149 Hom.: 2609

Bravo AF: 0.204

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.0
DANN	Benign	0.82

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: rs1122838; hg19: chr9-80263100;