rs1122838

Variant names:

• chr9-77648184-G-A
• rs1122838
• NM_004297.4:c.-391C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-77648184-G-A
• chr9-77648184-G-C
• chr9-77648184-G-T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.76).
• 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 rank	MANE	Protein	UniProt
GNA14	NM_004297.4	c.-391C>T		5_prime_UTR_variant	Exon 1 of 7	ENST00000341700.7	NP_004288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNA14	ENST00000341700.7	c.-391C>T		5_prime_UTR_variant	Exon 1 of 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

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

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

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: 62 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9344 AN: 67996

Other (OTH) AF: 0.222 AC: 470 AN: 2116

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.0
DANN	Benign	0.82
PhyloP100		-2.4
PromoterAI		-0.028	Neutral
Mutation Taster		=300/0	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: rs1122838; hg19: chr9-80263100;