22-37681711-A-G

Variant names:

• chr22-37681711-A-G
• rs2899292
• ENST00000493862.5:n.39A>G

Variant summary

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

The ENST00000493862.5(NOL12):​n.39A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,232 control chromosomes in the GnomAD database, including 11,175 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 0.38 (11159 hom., cov: 32)
  • Exomes 𝑓: 0.40 (16 hom.)
• Consequence: NOL12 ENST00000493862.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 19 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493862.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL12	ENST00000493862.5	TSL:5	n.39A>G		non_coding_transcript_exon	Exon 1 of 7

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57155 AN: 151906 Hom.: 11145 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.404 AC: 84 AN: 208 Hom.: 16 Cov.: 0 AF XY: 0.400 AC XY: 64 AN XY: 160

African (AFR) AF: 0.625 AC: 5 AN: 8

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.625 AC: 5 AN: 8

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.394 AC: 67 AN: 170

Other (OTH) AF: 0.300 AC: 3 AN: 10

GnomAD4 genome AF: 0.376 AC: 57205 AN: 152024 Hom.: 11159 Cov.: 32 AF XY: 0.376 AC XY: 27914 AN XY: 74298

African (AFR) AF: 0.484 AC: 20049 AN: 41458

American (AMR) AF: 0.387 AC: 5903 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5168

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4808

European-Finnish (FIN) AF: 0.297 AC: 3149 AN: 10586

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21263 AN: 67964

Other (OTH) AF: 0.371 AC: 782 AN: 2108

Alfa AF: 0.336 Hom.: 16159

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	10
DANN	Benign	0.90
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2899292; hg19: chr22-38077718;