ENST00000631185.2:c.331-2067G>T

Variant names:

• chrX-119588061-G-T
• rs2018358
• ENST00000631185.2:c.331-2067G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000631185.2(UBE2A):​c.331-2067G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.70 (19381 hom., 23239 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: UBE2A ENST00000631185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 2 publications found

Genes affected

UBE2A (HGNC:12472): (ubiquitin conjugating enzyme E2 A) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin-protein ligases. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is required for post-replicative DNA damage repair, and may play a role in transcriptional regulation. Mutations in this gene are associated with cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

UBE2A Gene-Disease associations (from GenCC):

• syndromic X-linked intellectual disability Nascimento type

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631185.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2A	ENST00000631185.2	TSL:5	c.331-2067G>T		intron	N/A	ENSP00000486153.1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 77992 AN: 110804 Hom.: 19377 Cov.: 23

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.726

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.704 AC: 78048 AN: 110861 Hom.: 19381 Cov.: 23 AF XY: 0.702 AC XY: 23239 AN XY: 33099

African (AFR) AF: 0.734 AC: 22396 AN: 30511

American (AMR) AF: 0.783 AC: 8178 AN: 10440

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 1825 AN: 2637

East Asian (EAS) AF: 0.760 AC: 2677 AN: 3522

South Asian (SAS) AF: 0.698 AC: 1873 AN: 2684

European-Finnish (FIN) AF: 0.612 AC: 3579 AN: 5850

Middle Eastern (MID) AF: 0.703 AC: 154 AN: 219

European-Non Finnish (NFE) AF: 0.675 AC: 35686 AN: 52833

Other (OTH) AF: 0.730 AC: 1090 AN: 1493

Alfa AF: 0.696 Hom.: 54998

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.45
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2018358; hg19: chrX-118722024;