chrX-38532551-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250349	ENST00000465127.1	TSL:5	c.172-133570T>C		intron	N/A	ENSP00000417050.1	B4E171
	UBTFL11	ENST00000428234.1	TSL:6	n.1624A>G		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4826995;

hg19: chrX-38391804;