16-88710834-C-A

Position:

• chr16-88710834-C-A

Variant summary

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

The NM_001012759.3(CTU2):​c.282+552C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 156,236 control chromosomes in the GnomAD database, including 48,539 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 0.79 (47371 hom., cov: 32)
  • Exomes 𝑓: 0.74 (1168 hom.)
• Consequence: CTU2 NM_001012759.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

CTU2 (HGNC:28005): (cytosolic thiouridylase subunit 2) This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

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 (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTU2	NM_001012759.3	c.282+552C>A		intron_variant		ENST00000453996.7	NP_001012777.1
CTU2	NM_001012762.3	c.282+552C>A		intron_variant			NP_001012780.1
CTU2	NM_001318507.2	c.282+552C>A		intron_variant			NP_001305436.1
CTU2	NM_001318513.2	c.21+552C>A		intron_variant			NP_001305442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTU2	ENST00000453996.7	c.282+552C>A		intron_variant		1	NM_001012759.3	ENSP00000388320	P2

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119701 AN: 151930 Hom.: 47344 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.820

GnomAD4 exome AF: 0.740 AC: 3099 AN: 4188 Hom.: 1168 Cov.: 0 AF XY: 0.746 AC XY: 1775 AN XY: 2380

Gnomad4 AFR exome AF: 0.729

Gnomad4 AMR exome AF: 0.799

Gnomad4 ASJ exome AF: 0.880

Gnomad4 EAS exome AF: 0.944

Gnomad4 SAS exome AF: 0.774

Gnomad4 FIN exome AF: 0.678

Gnomad4 NFE exome AF: 0.725

Gnomad4 OTH exome AF: 0.773

GnomAD4 genome AF: 0.788 AC: 119781 AN: 152048 Hom.: 47371 Cov.: 32 AF XY: 0.789 AC XY: 58675 AN XY: 74330

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.820

Alfa AF: 0.772 Hom.: 13056

Bravo AF: 0.794

Asia WGS AF: 0.848 AC: 2950 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	1.5
DANN	Benign	0.62

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: rs8052560; hg19: chr16-88777242;