rs4826995

Variant names:

• chrX-38532551-T-C
• rs4826995
• ENST00000465127.1:c.172-133570T>C

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.172-133570T>C variant causes a intron 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: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62
• Publications: 0 publications found

Genes affected

ENSG00000250349 (HGNC:):

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

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 = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBTFL11		n.38532551T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1	c.172-133570T>C		intron_variant	Intron 3 of 8	5		ENSP00000417050.1
UBTFL11	ENST00000428234.1	n.1624A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.443 AC: 48837 AN: 110137 Hom.: 10396 Cov.: 21

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

African (AFR) AF: 0.834 AC: 3032 AN: 3637

American (AMR) AF: 0.291 AC: 1229 AN: 4224

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1352 AN: 3967

East Asian (EAS) AF: 0.292 AC: 3400 AN: 11649

South Asian (SAS) AF: 0.235 AC: 494 AN: 2104

European-Finnish (FIN) AF: 0.226 AC: 2749 AN: 12168

Middle Eastern (MID) AF: 0.391 AC: 317 AN: 810

European-Non Finnish (NFE) AF: 0.307 AC: 24482 AN: 79680

Other (OTH) AF: 0.360 AC: 3023 AN: 8395

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

African (AFR) AF: 0.831 AC: 25005 AN: 30087

American (AMR) AF: 0.336 AC: 3494 AN: 10408

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 836 AN: 2622

East Asian (EAS) AF: 0.262 AC: 913 AN: 3488

South Asian (SAS) AF: 0.253 AC: 650 AN: 2573

European-Finnish (FIN) AF: 0.207 AC: 1224 AN: 5903

Middle Eastern (MID) AF: 0.370 AC: 78 AN: 211

European-Non Finnish (NFE) AF: 0.300 AC: 15795 AN: 52717

Other (OTH) AF: 0.418 AC: 626 AN: 1499

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
PhyloP100		3.6

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

Other links and lift over

dbSNP: rs4826995; hg19: chrX-38391804;