9-77637498-T-C

Position:

• chr9-77637498-T-C

Variant summary

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

The NM_004297.4(GNA14):​c.124+10172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,118 control chromosomes in the GnomAD database, including 11,498 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 0.33 (11498 hom., cov: 33)
• Consequence: GNA14 NM_004297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNA14	NM_004297.4	c.124+10172A>G		intron_variant		ENST00000341700.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA14	ENST00000341700.7	c.124+10172A>G		intron_variant		1	NM_004297.4	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49880 AN: 152000 Hom.: 11455 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.329 AC: 49983 AN: 152118 Hom.: 11498 Cov.: 33 AF XY: 0.338 AC XY: 25110 AN XY: 74384

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.317

Alfa AF: 0.184 Hom.: 4734

Bravo AF: 0.350

Asia WGS AF: 0.501 AC: 1741 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.83

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: rs6560608; hg19: chr9-80252414;