7-93924029-A-G

Variant names:

• chr7-93924029-A-G
• rs180236
• NM_004126.4:c.96+1796A>G

Variant summary

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

The NM_004126.4(GNG11):​c.96+1796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,072 control chromosomes in the GnomAD database, including 32,550 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 0.65 (32550 hom., cov: 32)
• Consequence: GNG11 NM_004126.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908
• Publications: 7 publications found

Genes affected

GNG11 (HGNC:4403): (G protein subunit gamma 11) This gene is a member of the guanine nucleotide-binding protein (G protein) gamma family and encodes a lipid-anchored, cell membrane protein. As a member of the heterotrimeric G protein complex, this protein plays a role in this transmembrane signaling system. This protein is also subject to carboxyl-terminal processing. Decreased expression of this gene is associated with splenic marginal zone lymphomas. [provided by RefSeq, Jul 2008]

ENSG00000306701 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNG11	NM_004126.4	c.96+1796A>G		intron_variant	Intron 1 of 1	ENST00000248564.6	NP_004117.1
LOC105375402	XR_927751.3	n.380-7509T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG11	ENST00000248564.6	c.96+1796A>G		intron_variant	Intron 1 of 1	1	NM_004126.4	ENSP00000248564.4
ENSG00000306701	ENST00000820276.1	n.301-11705T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99055 AN: 151954 Hom.: 32535 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.652 AC: 99107 AN: 152072 Hom.: 32550 Cov.: 32 AF XY: 0.658 AC XY: 48923 AN XY: 74324

African (AFR) AF: 0.640 AC: 26532 AN: 41472

American (AMR) AF: 0.720 AC: 11000 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2351 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4685 AN: 5182

South Asian (SAS) AF: 0.681 AC: 3271 AN: 4806

European-Finnish (FIN) AF: 0.667 AC: 7036 AN: 10552

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41982 AN: 67988

Other (OTH) AF: 0.657 AC: 1388 AN: 2112

Alfa AF: 0.633 Hom.: 43252

Bravo AF: 0.655

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.91
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: rs180236; hg19: chr7-93553341;