9-92321784-T-A

Variant names:

• chr9-92321784-T-A
• rs2274967
• NM_017948.6:c.203-38A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017948.6(NOL8):​c.203-38A>T variant causes a intron 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NOL8 NM_017948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 6 publications found

Genes affected

NOL8 (HGNC:23387): (nucleolar protein 8) NOL8 binds Ras-related GTP-binding proteins (see MIM 608267) and plays a role in cell growth (Sekiguchi et al., 2004 [PubMed 14660641]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017948.6. 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
	NOL8	NM_017948.6	MANE Select	c.203-38A>T		intron	N/A	NP_060418.4
	NOL8	NM_001438180.1		c.203-38A>T		intron	N/A	NP_001425109.1
	NOL8	NM_001438181.1		c.203-38A>T		intron	N/A	NP_001425110.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL8	ENST00000442668.7	TSL:1 MANE Select	c.203-38A>T		intron	N/A	ENSP00000401177.2
	NOL8	ENST00000358855.8	TSL:1	c.-2-38A>T		intron	N/A	ENSP00000351723.4
	NOL8	ENST00000542053.5	TSL:5	c.-2-38A>T		intron	N/A	ENSP00000440709.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 56

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.40
PhyloP100		-0.32

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: rs2274967; hg19: chr9-95084066;