X-119588061-G-T

Position:

• chrX-119588061-G-T

Variant summary

Our verdict is Likely benign. Variant got -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

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2A	ENST00000631185.2	c.331-2067G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.704 AC: 77992 AN: 110804 Hom.: 19377 Cov.: 23 AF XY: 0.702 AC XY: 23183 AN XY: 33032

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

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.730

Alfa AF: 0.691 Hom.: 40033

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018358; hg19: chrX-118722024;