NM_001010906.2:c.712-1140G>A

Variant names:

• chr8-28065871-C-T
• rs4732812
• NM_001010906.2:c.712-1140G>A

Variant summary

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

The NM_001010906.2(NUGGC):​c.712-1140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,086 control chromosomes in the GnomAD database, including 5,812 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 0.27 (5812 hom., cov: 32)
• Consequence: NUGGC NM_001010906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 11 publications found

Genes affected

NUGGC (HGNC:33550): (nuclear GTPase, germinal center associated) Enables GTPase activity. Involved in cellular response to lipopolysaccharide; negative regulation of apoptotic process; and regulation of nuclear cell cycle DNA replication. Predicted to be located in nucleus. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUGGC	NM_001010906.2	c.712-1140G>A		intron_variant	Intron 6 of 18	ENST00000413272.7	NP_001010906.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUGGC	ENST00000413272.7	c.712-1140G>A		intron_variant	Intron 6 of 18	5	NM_001010906.2	ENSP00000408697.2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41320 AN: 151968 Hom.: 5810 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.272 AC: 41355 AN: 152086 Hom.: 5812 Cov.: 32 AF XY: 0.270 AC XY: 20070 AN XY: 74334

African (AFR) AF: 0.256 AC: 10614 AN: 41484

American (AMR) AF: 0.299 AC: 4572 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3472

East Asian (EAS) AF: 0.142 AC: 736 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4814

European-Finnish (FIN) AF: 0.253 AC: 2676 AN: 10568

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19460 AN: 67984

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.280 Hom.: 26070

Bravo AF: 0.277

Asia WGS AF: 0.207 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.68
PhyloP100		-0.35
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: rs4732812; hg19: chr8-27923388;