16-67175352-A-G

Variant names:

• chr16-67175352-A-G
• rs8057598
• NM_001276309.3:c.*298A>G

Variant summary

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

The NM_001276309.3(NOL3):​c.*298A>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 0.101 in 1,293,680 control chromosomes in the GnomAD database, including 16,053 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 0.22 (7602 hom., cov: 33)
  • Exomes 𝑓: 0.085 (8451 hom.)
• Consequence: NOL3 NM_001276309.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 18 publications found

Genes affected

NOL3 (HGNC:7869): (nucleolar protein 3) This gene encodes an anti-apoptotic protein that has been shown to down-regulate the enzyme activities of caspase 2, caspase 8 and tumor protein p53. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

MATCAP1 (HGNC:34408): (microtubule associated tyrosine carboxypeptidase 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276309.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL3	NM_001276309.3	MANE Select	c.*298A>G		3_prime_UTR	Exon 4 of 4	NP_001263238.1
	NOL3	NM_001394979.1		c.*255A>G		3_prime_UTR	Exon 4 of 4	NP_001381908.1
	NOL3	NM_001185057.3		c.*255A>G		3_prime_UTR	Exon 4 of 4	NP_001171986.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL3	ENST00000564992.2	TSL:2 MANE Select	c.*298A>G		3_prime_UTR	Exon 4 of 4	ENSP00000457720.2
	NOL3	ENST00000568146.1	TSL:1	c.*255A>G		3_prime_UTR	Exon 4 of 4	ENSP00000454598.1
	NOL3	ENST00000568503.1	TSL:5	n.1182A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33481 AN: 152002 Hom.: 7567 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.0851 AC: 97157 AN: 1141560 Hom.: 8451 Cov.: 30 AF XY: 0.0851 AC XY: 46284 AN XY: 544184

African (AFR) AF: 0.616 AC: 15586 AN: 25282

American (AMR) AF: 0.102 AC: 1191 AN: 11650

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 620 AN: 15580

East Asian (EAS) AF: 0.0194 AC: 554 AN: 28496

South Asian (SAS) AF: 0.173 AC: 6259 AN: 36270

European-Finnish (FIN) AF: 0.111 AC: 2443 AN: 21978

Middle Eastern (MID) AF: 0.0945 AC: 291 AN: 3078

European-Non Finnish (NFE) AF: 0.0686 AC: 65413 AN: 953076

Other (OTH) AF: 0.104 AC: 4800 AN: 46150

GnomAD4 genome AF: 0.221 AC: 33576 AN: 152120 Hom.: 7602 Cov.: 33 AF XY: 0.219 AC XY: 16317 AN XY: 74374

African (AFR) AF: 0.585 AC: 24272 AN: 41458

American (AMR) AF: 0.116 AC: 1770 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5178

South Asian (SAS) AF: 0.169 AC: 816 AN: 4830

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0691 AC: 4696 AN: 67966

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.123 Hom.: 3289

Bravo AF: 0.233

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.66
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs8057598; hg19: chr16-67209255;