17-44207100-ATTTTT-ATTTTTT

Variant names:

• chr17-44207100-A-AT
• rs374363130
• NM_014233.4:c.*141dupA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_014233.4(UBTF):​c.*141dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 798,076 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00096 (0 hom., cov: 29)
  • Exomes 𝑓: 0.021 (0 hom.)
• Consequence: UBTF NM_014233.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

UBTF (HGNC:12511): (upstream binding transcription factor) This gene encodes a member of the HMG-box DNA-binding protein family. The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3, 11 and X and the long arm of chromosome 11. [provided by RefSeq, Aug 2011]

ATXN7L3-AS1 (HGNC:55298): (ATXN7L3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.021 (13905/661170) while in subpopulation NFE AF= 0.0235 (10966/466864). AF 95% confidence interval is 0.0231. There are 0 homozygotes in gnomad4_exome. There are 6989 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 131 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBTF	NM_014233.4	c.*141dupA		3_prime_UTR_variant	Exon 21 of 21	ENST00000436088.6	NP_055048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBTF	ENST00000436088	c.*141dupA		3_prime_UTR_variant	Exon 21 of 21	2	NM_014233.4	ENSP00000390669.1

Frequencies

GnomAD3 genomes AF: 0.000957 AC: 131 AN: 136912 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00109

Gnomad ASJ AF: 0.00215

Gnomad EAS AF: 0.00294

Gnomad SAS AF: 0.00162

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000751

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0210 AC: 13905 AN: 661170 Hom.: 0 Cov.: 0 AF XY: 0.0206 AC XY: 6989 AN XY: 338550

Gnomad4 AFR exome AF: 0.0184

Gnomad4 AMR exome AF: 0.0114

Gnomad4 ASJ exome AF: 0.0155

Gnomad4 EAS exome AF: 0.0112

Gnomad4 SAS exome AF: 0.0187

Gnomad4 FIN exome AF: 0.0103

Gnomad4 NFE exome AF: 0.0235

Gnomad4 OTH exome AF: 0.0183

GnomAD4 genome AF: 0.000957 AC: 131 AN: 136906 Hom.: 0 Cov.: 29 AF XY: 0.000890 AC XY: 59 AN XY: 66268

Gnomad4 AFR AF: 0.000644

Gnomad4 AMR AF: 0.00109

Gnomad4 ASJ AF: 0.00215

Gnomad4 EAS AF: 0.00295

Gnomad4 SAS AF: 0.00163

Gnomad4 FIN AF: 0.00211

Gnomad4 NFE AF: 0.000751

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs374363130; hg19: chr17-42284468;