rs9409664

Variant names:

• chr9-92307813-A-G
• rs9409664
• NM_017948.6:c.2687-789T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017948.6(NOL8):​c.2687-789T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,032 control chromosomes in the GnomAD database, including 28,530 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 (28530 hom., cov: 32)
• Consequence: NOL8 NM_017948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL8	NM_017948.6	c.2687-789T>C		intron_variant	Intron 10 of 16	ENST00000442668.7	NP_060418.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL8	ENST00000442668.7	c.2687-789T>C		intron_variant	Intron 10 of 16	1	NM_017948.6	ENSP00000401177.2
NOL8	ENST00000542053.5	c.2483-789T>C		intron_variant	Intron 9 of 15	5		ENSP00000440709.1
NOL8	ENST00000432670.6	c.2687-789T>C		intron_variant	Intron 10 of 12	5		ENSP00000414112.2
NOL8	ENST00000360868.7	n.*2542-789T>C		intron_variant	Intron 10 of 16	2		ENSP00000354115.3
NOL8	ENST00000434228.5	n.*2979-789T>C		intron_variant	Intron 12 of 12	2		ENSP00000415750.1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88727 AN: 151914 Hom.: 28470 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.584 AC: 88839 AN: 152032 Hom.: 28530 Cov.: 32 AF XY: 0.579 AC XY: 42996 AN XY: 74298

African (AFR) AF: 0.861 AC: 35748 AN: 41506

American (AMR) AF: 0.489 AC: 7460 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5170

South Asian (SAS) AF: 0.519 AC: 2499 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4856 AN: 10536

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33402 AN: 67950

Other (OTH) AF: 0.554 AC: 1171 AN: 2114

Alfa AF: 0.523 Hom.: 62486

Bravo AF: 0.597

Asia WGS AF: 0.401 AC: 1392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.51
PhyloP100		-0.96
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: rs9409664; hg19: chr9-95070095; COSMIC: COSV62638699;