19-3159771-A-G

Variant names:

• chr19-3159771-A-G
• rs11880198
• NM_002068.4:c.898+1890A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002068.4(GNA15):​c.898+1890A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,214 control chromosomes in the GnomAD database, including 2,576 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 0.18 (2576 hom., cov: 32)
• Consequence: GNA15 NM_002068.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 21 publications found

Genes affected

GNA15 (HGNC:4383): (G protein subunit alpha 15) Enables G protein-coupled receptor binding activity. Involved in positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway. Predicted to be located in plasma membrane. Predicted to be part of heterotrimeric G-protein complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNA15	NM_002068.4	c.898+1890A>G		intron_variant	Intron 6 of 6	ENST00000262958.4	NP_002059.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNA15	ENST00000262958.4	c.898+1890A>G		intron_variant	Intron 6 of 6	1	NM_002068.4	ENSP00000262958.2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26925 AN: 152096 Hom.: 2573 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.177 AC: 26954 AN: 152214 Hom.: 2576 Cov.: 32 AF XY: 0.176 AC XY: 13088 AN XY: 74424

African (AFR) AF: 0.204 AC: 8482 AN: 41522

American (AMR) AF: 0.127 AC: 1939 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3472

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5194

South Asian (SAS) AF: 0.112 AC: 543 AN: 4830

European-Finnish (FIN) AF: 0.216 AC: 2285 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12588 AN: 68012

Other (OTH) AF: 0.170 AC: 360 AN: 2116

Alfa AF: 0.175 Hom.: 10985

Bravo AF: 0.170

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.36
PhyloP100		-0.12
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: rs11880198; hg19: chr19-3159769;