rs10509672

Variant names:

• chr10-94356200-G-C
• rs10509672
• NM_022451.11:c.565+335C>G

Variant summary

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

The NM_022451.11(NOC3L):​c.565+335C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 152,214 control chromosomes in the GnomAD database, including 388 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 0.064 (388 hom., cov: 32)
• Consequence: NOC3L NM_022451.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 1 publications found

Genes affected

NOC3L (HGNC:24034): (NOC3 like DNA replication regulator) Enables RNA binding activity. Predicted to be involved in DNA replication initiation. Predicted to act upstream of or within fat cell differentiation. Located in mitochondrion; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOC3L	NM_022451.11	c.565+335C>G		intron_variant	Intron 5 of 20	ENST00000371361.3	NP_071896.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOC3L	ENST00000371361.3	c.565+335C>G		intron_variant	Intron 5 of 20	1	NM_022451.11	ENSP00000360412.3
NOC3L	ENST00000463649.5	n.1417+335C>G		intron_variant	Intron 4 of 9	2

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9652 AN: 152096 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0635 AC: 9667 AN: 152214 Hom.: 388 Cov.: 32 AF XY: 0.0598 AC XY: 4451 AN XY: 74410

African (AFR) AF: 0.0223 AC: 925 AN: 41554

American (AMR) AF: 0.0747 AC: 1142 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3472

East Asian (EAS) AF: 0.0917 AC: 476 AN: 5190

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4822

European-Finnish (FIN) AF: 0.0318 AC: 337 AN: 10596

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0838 AC: 5698 AN: 67980

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0708 Hom.: 61

Bravo AF: 0.0658

Asia WGS AF: 0.0660 AC: 227 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.11
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: rs10509672; hg19: chr10-96115957;