2-10575262-T-C

Position:

• chr2-10575262-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024894.4(NOL10):​c.1947+2374A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,170 control chromosomes in the GnomAD database, including 6,508 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 0.25 (6508 hom., cov: 33)
• Consequence: NOL10 NM_024894.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.28

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOL10	NM_024894.4	c.1947+2374A>G		intron_variant		ENST00000381685.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOL10	ENST00000381685.10	c.1947+2374A>G		intron_variant		1	NM_024894.4	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37615 AN: 152052 Hom.: 6486 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.248 AC: 37685 AN: 152170 Hom.: 6508 Cov.: 33 AF XY: 0.255 AC XY: 18941 AN XY: 74412

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.206

Alfa AF: 0.225 Hom.: 815

Bravo AF: 0.266

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.038
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs6757809; hg19: chr2-10715388;