chr2-10603420-A-G

Variant names:

• chr2-10603420-A-G
• rs1309
• NM_024894.4:c.1154-263T>C

Variant summary

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

The NM_024894.4(NOL10):​c.1154-263T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,952 control chromosomes in the GnomAD database, including 27,619 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 0.59 (27619 hom., cov: 31)
• Consequence: NOL10 NM_024894.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 12 publications found

Genes affected

NOL10 (HGNC:25862): (nucleolar protein 10) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000234818 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL10	NM_024894.4	c.1154-263T>C		intron_variant	Intron 14 of 20	ENST00000381685.10	NP_079170.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL10	ENST00000381685.10	c.1154-263T>C		intron_variant	Intron 14 of 20	1	NM_024894.4	ENSP00000371101.5

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89840 AN: 151834 Hom.: 27579 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.592 AC: 89926 AN: 151952 Hom.: 27619 Cov.: 31 AF XY: 0.596 AC XY: 44234 AN XY: 74258

African (AFR) AF: 0.740 AC: 30677 AN: 41440

American (AMR) AF: 0.557 AC: 8493 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3193 AN: 5176

South Asian (SAS) AF: 0.431 AC: 2069 AN: 4804

European-Finnish (FIN) AF: 0.669 AC: 7049 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35345 AN: 67950

Other (OTH) AF: 0.520 AC: 1099 AN: 2114

Alfa AF: 0.541 Hom.: 13388

Bravo AF: 0.593

Asia WGS AF: 0.510 AC: 1774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		-0.034
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: rs1309; hg19: chr2-10743546;