rs9288967

chr3-112998472-A-Cchr3-112998472-A-T

Variant summary

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

The NM_014170.4(GTPBP8):c.667-974A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,892 control chromosomes in the GnomAD database, including 29,238 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 0.58 (29238 hom., cov: 31)
• Consequence: GTPBP8 NM_014170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

Genes affected

GTPBP8 (HGNC:25007): (GTP binding protein 8 (putative)) Predicted to enable GTP binding activity and metal ion binding activity. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GTPBP8	NM_014170.4	c.667-974A>C		intron_variant		ENST00000383678.8
GTPBP8	NM_138485.2	c.568-974A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GTPBP8	ENST00000383678.8	c.667-974A>C		intron_variant		1	NM_014170.4	P1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88200 AN: 151776 Hom.: 29229 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.581 AC: 88220 AN: 151892 Hom.: 29238 Cov.: 31 AF XY: 0.577 AC XY: 42803 AN XY: 74228

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.622

Alfa AF: 0.719 Hom.: 51959

Bravo AF: 0.569

Asia WGS AF: 0.490 AC: 1704 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	1.4
Dann	Benign	0.63

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: rs9288967; hg19: chr3-112717319;