14-51900357-C-T

Variant names:

• chr14-51900357-C-T
• rs11157865
• NM_053064.5:c.-30+22700C>T

Variant summary

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

The NM_053064.5(GNG2):​c.-30+22700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,506 control chromosomes in the GnomAD database, including 18,736 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 0.49 (18736 hom., cov: 29)
• Consequence: GNG2 NM_053064.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 3 publications found

Genes affected

GNG2 (HGNC:4404): (G protein subunit gamma 2) This gene encodes one of the gamma subunits of a guanine nucleotide-binding protein. Such proteins are involved in signaling mechanisms across membranes. Various subunits forms heterodimers which then interact with the different signal molecules. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNG2	NM_053064.5	c.-30+22700C>T		intron_variant	Intron 2 of 3	ENST00000556766.6	NP_444292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG2	ENST00000556766.6	c.-30+22700C>T		intron_variant	Intron 2 of 3	1	NM_053064.5	ENSP00000451231.1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73622 AN: 151388 Hom.: 18713 Cov.: 29

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.486 AC: 73680 AN: 151506 Hom.: 18736 Cov.: 29 AF XY: 0.488 AC XY: 36103 AN XY: 74008

African (AFR) AF: 0.630 AC: 25975 AN: 41198

American (AMR) AF: 0.447 AC: 6808 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1294 AN: 3458

East Asian (EAS) AF: 0.458 AC: 2363 AN: 5162

South Asian (SAS) AF: 0.472 AC: 2269 AN: 4810

European-Finnish (FIN) AF: 0.483 AC: 5046 AN: 10458

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28470 AN: 67874

Other (OTH) AF: 0.443 AC: 933 AN: 2108

Alfa AF: 0.422 Hom.: 18013

Bravo AF: 0.488

Asia WGS AF: 0.449 AC: 1562 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		0.052
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: rs11157865; hg19: chr14-52367075;