dbSNP rs1122838: GNA14:c.-391C>T (chr9-77648184-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Publications

5 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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.-391C>T		5_prime_UTR	Exon 1 of 7	NP_004288.1	O95837

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA14	ENST00000341700.7	TSL:1 MANE Select	c.-391C>T		5_prime_UTR	Exon 1 of 7	ENSP00000365807.4	O95837

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30101

AN:

152028

Hom.:

3303

Cov.:

show subpopulations

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.:

AF XY:

0.174

AC XY:

13269

AN XY:

76442

show subpopulations

African (AFR)

AF:

0.270

AC:

489

AN:

1814

American (AMR)

AF:

0.218

AC:

687

AN:

3148

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

694

AN:

3694

East Asian (EAS)

AF:

0.232

AC:

707

AN:

3052

South Asian (SAS)

AF:

0.249

AC:

6284

AN:

25284

European-Finnish (FIN)

AF:

0.183

AC:

1629

AN:

8906

Middle Eastern (MID)

AF:

0.187

AC:

109

AN:

582

European-Non Finnish (NFE)

AF:

0.134

AC:

11968

AN:

89012

Other (OTH)

AF:

0.167

AC:

1306

AN:

7838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

927

1854

2782

3709

4636

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

222

296

370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.198

AC:

30150

AN:

152146

Hom.:

3318

Cov.:

AF XY:

0.201

AC XY:

14952

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.269

AC:

11180

AN:

41528

American (AMR)

AF:

0.226

AC:

3456

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

671

AN:

3472

East Asian (EAS)

AF:

0.273

AC:

1396

AN:

5114

South Asian (SAS)

AF:

0.272

AC:

1312

AN:

4824

European-Finnish (FIN)

AF:

0.200

AC:

2124

AN:

10594

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.137

AC:

9344

AN:

67996

Other (OTH)

AF:

0.222

AC:

470

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1230

2461

3691

4922

6152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.156

Hom.:

3635

Bravo

AF:

0.204

Asia WGS

AF:

0.301

AC:

1044

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.0

(source)

DANN

Benign

0.82

PhyloP100

-2.4

PromoterAI

-0.028

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over