rs4826995

Positions:

• chrX-38532551-T-C

Variant summary

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

The ENST00000428234.1(UBTFL11):​n.1624A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.376 in 236,824 control chromosomes in the GnomAD database, including 15,778 homozygotes. There are 22,917 hemizygotes in GnomAD. 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 0.44 (10402 hom., 13525 hem., cov: 21)
  • Exomes 𝑓: 0.32 (5376 hom. 9392 hem.)
• Consequence: UBTFL11 ENST00000428234.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62

Genes affected

UBTFL11 (HGNC:50288): (UBTF like 11 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -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 = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBTFL11	ENST00000428234.1	n.1624A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 48837 AN: 110137 Hom.: 10396 Cov.: 21 AF XY: 0.416 AC XY: 13478 AN XY: 32411

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.316 AC: 40078 AN: 126634 Hom.: 5376 Cov.: 2 AF XY: 0.333 AC XY: 9392 AN XY: 28232

Gnomad4 AFR exome AF: 0.834

Gnomad4 AMR exome AF: 0.291

Gnomad4 ASJ exome AF: 0.341

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.235

Gnomad4 FIN exome AF: 0.226

Gnomad4 NFE exome AF: 0.307

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.444 AC: 48892 AN: 110190 Hom.: 10402 Cov.: 21 AF XY: 0.416 AC XY: 13525 AN XY: 32474

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.418

Alfa AF: 0.442 Hom.: 4140

Bravo AF: 0.476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.7
DANN	Benign	0.68

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: rs4826995; hg19: chrX-38391804;