rs16998437

chr22-37692388-T-G

Variant summary

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

The NM_024313.3(NOL12):c.*1052T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00998 in 398,120 control chromosomes in the GnomAD database, including 148 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 0.021 (119 hom., cov: 33)
  • Exomes 𝑓: 0.0029 (29 hom.)
• Consequence: NOL12 NM_024313.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

NOL12 (HGNC:28585): (nucleolar protein 12) Enables identical protein binding activity. Predicted to be active 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOL12	NM_024313.3	c.*1052T>G		3_prime_UTR_variant	6/6	ENST00000359114.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOL12	ENST00000359114.9	c.*1052T>G		3_prime_UTR_variant	6/6	1	NM_024313.3	P1
NOL12	ENST00000611699.1	c.*89-944T>G		intron_variant		1		P1
NOL12	ENST00000438329.5	c.*89-944T>G		intron_variant, NMD_transcript_variant		1
NOL12	ENST00000493862.5	n.868-944T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3247 AN: 152108 Hom.: 119 Cov.: 33

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00675

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.0163

GnomAD4 exome AF: 0.00292 AC: 718 AN: 245894 Hom.: 29 Cov.: 0 AF XY: 0.00254 AC XY: 317 AN XY: 124634

Gnomad4 AFR exome AF: 0.0763

Gnomad4 AMR exome AF: 0.00484

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000127

Gnomad4 OTH exome AF: 0.00696

GnomAD4 genome AF: 0.0214 AC: 3254 AN: 152226 Hom.: 119 Cov.: 33 AF XY: 0.0203 AC XY: 1514 AN XY: 74434

Gnomad4 AFR AF: 0.0747

Gnomad4 AMR AF: 0.00674

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00643 Hom.: 30

Bravo AF: 0.0245

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.39
Dann	Benign	0.61

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: rs16998437; hg19: chr22-38088395;