rs16998437

Variant names:

• chr22-37692388-T-G
• rs16998437
• NM_024313.3:c.*1052T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ENSG00000100101 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024313.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL12	NM_024313.3	MANE Select	c.*1052T>G		3_prime_UTR	Exon 6 of 6	NP_077289.1	Q9UGY1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL12	ENST00000359114.9	TSL:1 MANE Select	c.*1052T>G		3_prime_UTR	Exon 6 of 6	ENSP00000352021.4	Q9UGY1
	NOL12	ENST00000611699.1	TSL:1	c.*89-944T>G		intron	N/A	ENSP00000482349.1	Q9UGY1
	NOL12	ENST00000438329.5	TSL:1	n.*89-944T>G		intron	N/A	ENSP00000403059.1	Q9UGY1

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

African (AFR) AF: 0.0763 AC: 548 AN: 7184

American (AMR) AF: 0.00484 AC: 36 AN: 7436

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9240

East Asian (EAS) AF: 0.00 AC: 0 AN: 22890

South Asian (SAS) AF: 0.00 AC: 0 AN: 2584

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20812

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1296

European-Non Finnish (NFE) AF: 0.000127 AC: 20 AN: 158084

Other (OTH) AF: 0.00696 AC: 114 AN: 16368

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

African (AFR) AF: 0.0747 AC: 3104 AN: 41530

American (AMR) AF: 0.00674 AC: 103 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000132 AC: 9 AN: 68014

Other (OTH) AF: 0.0161 AC: 34 AN: 2112

Alfa AF: 0.00947 Hom.: 90

Bravo AF: 0.0245

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.61
PhyloP100		-1.3
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: rs16998437; hg19: chr22-38088395;