NM_033107.4:c.33+1672A>G

Variant names:

• chr7-90348446-A-G
• rs42648
• NM_033107.4:c.33+1672A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033107.4(GTPBP10):​c.33+1672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,062 control chromosomes in the GnomAD database, including 21,367 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 0.52 (21367 hom., cov: 31)
• Consequence: GTPBP10 NM_033107.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

GTPBP10 (HGNC:25106): (GTP binding protein 10) Small G proteins, such as GTPBP10, act as molecular switches that play crucial roles in the regulation of fundamental cellular processes such as protein synthesis, nuclear transport, membrane trafficking, and signal transduction (Hirano et al., 2006 [PubMed 17054726]).[supplied by OMIM, Mar 2008]

LOC107986715 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GTPBP10	NM_033107.4	c.33+1672A>G		intron_variant	Intron 1 of 9	ENST00000222511.11	NP_149098.2
GTPBP10	NM_001042717.3	c.33+1672A>G		intron_variant	Intron 1 of 7		NP_001036182.1
LOC107986715	XR_001744961.2	n.3333-6695T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GTPBP10	ENST00000222511.11	c.33+1672A>G		intron_variant	Intron 1 of 9	1	NM_033107.4	ENSP00000222511.7

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78664 AN: 151944 Hom.: 21350 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.518 AC: 78718 AN: 152062 Hom.: 21367 Cov.: 31 AF XY: 0.515 AC XY: 38277 AN XY: 74320

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.520

Alfa AF: 0.574 Hom.: 3209

Bravo AF: 0.498

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs42648; hg19: chr7-89977760;