rs7284767

Positions:

• chr22-30973338-G-A

Variant summary

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

The ENST00000644773.3(TUG1):​c.*2445G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,998 control chromosomes in the GnomAD database, including 13,463 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 0.40 (13462 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: TUG1 ENST00000644773.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

TUG1 (HGNC:26066): (taurine up-regulated 1) Predicted to act upstream of or within photoreceptor cell development and regulation of gene expression. Predicted to be active in nucleus. Biomarker of Huntington's disease. [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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUG1	NM_001396518.1	c.*2445G>A		3_prime_UTR_variant	2/3	ENST00000644773.3
TUG1	NR_152868.2	n.731G>A		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUG1	ENST00000644773.3	c.*2445G>A		3_prime_UTR_variant	2/3		NM_001396518.1	P1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61365 AN: 151876 Hom.: 13444 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.379

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.404 AC: 61423 AN: 151994 Hom.: 13462 Cov.: 32 AF XY: 0.403 AC XY: 29952 AN XY: 74292

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.375

Alfa AF: 0.356 Hom.: 2430

Bravo AF: 0.413

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7284767; hg19: chr22-31369324;