rs42648

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-90348446-A-G
• chr7-90348446-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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]

ENSG00000309151 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033107.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTPBP10	NM_033107.4	MANE Select	c.33+1672A>G		intron	N/A	NP_149098.2
	GTPBP10	NM_001042717.3		c.33+1672A>G		intron	N/A	NP_001036182.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTPBP10	ENST00000222511.11	TSL:1 MANE Select	c.33+1672A>G		intron	N/A	ENSP00000222511.7
	GTPBP10	ENST00000257659.12	TSL:1	c.33+1672A>G		intron	N/A	ENSP00000257659.8
	GTPBP10	ENST00000380058.7	TSL:1	n.33+1672A>G		intron	N/A	ENSP00000369398.3

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

African (AFR) AF: 0.412 AC: 17063 AN: 41460

American (AMR) AF: 0.453 AC: 6922 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1841 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1167 AN: 5172

South Asian (SAS) AF: 0.470 AC: 2268 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6577 AN: 10552

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41073 AN: 67990

Other (OTH) AF: 0.520 AC: 1098 AN: 2110

Alfa AF: 0.515 Hom.: 7640

Bravo AF: 0.498

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.66
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: rs42648; hg19: chr7-89977760;