14-93206951-A-C

Variant names:

• chr14-93206951-A-C
• NM_032490.5:c.87T>G
• GON7 p.Pro29Pro

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_032490.5(GON7):​c.87T>G​(p.Pro29Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P29P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GON7 NM_032490.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 0 publications found

Genes affected

GON7 (HGNC:20356): (GON7 subunit of KEOPS complex) Located in cytosol; nucleolus; and nucleoplasm. Part of EKC/KEOPS complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259066 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.022).
• BP7: Synonymous conserved (PhyloP=0.685 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032490.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GON7	NM_032490.5	MANE Select	c.87T>G	p.Pro29Pro	synonymous	Exon 1 of 2	NP_115879.2	Q9BXV9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GON7	ENST00000306954.5	TSL:1 MANE Select	c.87T>G	p.Pro29Pro	synonymous	Exon 1 of 2	ENSP00000306320.4	Q9BXV9
	ENSG00000259066	ENST00000557574.1	TSL:4	c.208-2873A>C		intron	N/A	ENSP00000451369.1	G3V3Q6
	GON7	ENST00000923944.1		c.87T>G	p.Pro29Pro	synonymous	Exon 1 of 2	ENSP00000594003.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		0.69
PromoterAI		-0.010	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr14-93673296;