rs9288967

Variant names:

• chr3-112998472-A-C
• rs9288967
• NM_014170.4:c.667-974A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-112998472-A-C
• chr3-112998472-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GTPBP8	NM_014170.4	c.667-974A>C		intron_variant	Intron 4 of 5	ENST00000383678.8	NP_054889.2
GTPBP8	NM_138485.2	c.568-974A>C		intron_variant	Intron 3 of 4		NP_612494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GTPBP8	ENST00000383678.8	c.667-974A>C		intron_variant	Intron 4 of 5	1	NM_014170.4	ENSP00000373176.2

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

African (AFR) AF: 0.254 AC: 10530 AN: 41382

American (AMR) AF: 0.708 AC: 10814 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1762 AN: 5148

South Asian (SAS) AF: 0.600 AC: 2886 AN: 4810

European-Finnish (FIN) AF: 0.636 AC: 6688 AN: 10512

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.748 AC: 50868 AN: 67990

Other (OTH) AF: 0.622 AC: 1314 AN: 2114

Alfa AF: 0.706 Hom.: 64283

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
PhyloP100		-0.67
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: rs9288967; hg19: chr3-112717319;