rs11145462

Variant names:

• chr9-77528194-G-A
• rs11145462
• NM_004297.4:c.309+875C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-77528194-G-A
• chr9-77528194-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA14	NM_004297.4	MANE Select	c.309+875C>T		intron	N/A	NP_004288.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA14	ENST00000341700.7	TSL:1 MANE Select	c.309+875C>T		intron	N/A	ENSP00000365807.4

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

African (AFR) AF: 0.344 AC: 14210 AN: 41360

American (AMR) AF: 0.584 AC: 8917 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2383 AN: 5162

South Asian (SAS) AF: 0.506 AC: 2427 AN: 4800

European-Finnish (FIN) AF: 0.552 AC: 5818 AN: 10538

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.530 AC: 35983 AN: 67946

Other (OTH) AF: 0.496 AC: 1044 AN: 2104

Alfa AF: 0.509 Hom.: 64090

Bravo AF: 0.477

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.84
PhyloP100		-1.2
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: rs11145462; hg19: chr9-80143110;