X-119851748-C-CTTTTTTTTTTT

Variant names:

• chrX-119851748-C-CTTTTTTTTTTT
• rs55712755
• NM_080632.3:c.263+8_263+18dupAAAAAAAAAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_080632.3(UPF3B):​c.263+8_263+18dupAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00093 (4 hom., 9 hem., cov: 0)
  • Exomes 𝑓: 0.014 (96 hom. 648 hem.)
  • Failed GnomAD Quality Control
• Consequence: UPF3B NM_080632.3 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0650
• Publications: 0 publications found

Genes affected

UPF3B (HGNC:20439): (UPF3B regulator of nonsense mediated mRNA decay) This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

UPF3B Gene-Disease associations (from GenCC):

• syndromic X-linked intellectual disability 14

  Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• X-linked complex neurodevelopmental disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• X-linked intellectual disability with marfanoid habitus

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP6: Variant X-119851748-C-CTTTTTTTTTTT is Benign according to our data. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-119851748-C-CTTTTTTTTTTT is described in CliVar as Likely_benign. Clinvar id is 1615705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPF3B	NM_080632.3	c.263+8_263+18dupAAAAAAAAAAA		intron_variant	Intron 2 of 10	ENST00000276201.7	NP_542199.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UPF3B	ENST00000276201.7	c.263+18_263+19insAAAAAAAAAAA		intron_variant	Intron 2 of 10	1	NM_080632.3	ENSP00000276201.3
UPF3B	ENST00000345865.6	c.263+18_263+19insAAAAAAAAAAA		intron_variant	Intron 2 of 9	1		ENSP00000245418.2

Frequencies

GnomAD3 genomes AF: 0.000934 AC: 60 AN: 64221 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00260

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000680

Gnomad ASJ AF: 0.000500

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000579

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0142 AC: 6759 AN: 475665 Hom.: 96 Cov.: 0 AF XY: 0.00475 AC XY: 648 AN XY: 136407

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0281 AC: 200 AN: 7127

American (AMR) AF: 0.0374 AC: 418 AN: 11172

Ashkenazi Jewish (ASJ) AF: 0.0171 AC: 186 AN: 10876

East Asian (EAS) AF: 0.0501 AC: 684 AN: 13664

South Asian (SAS) AF: 0.0169 AC: 453 AN: 26772

European-Finnish (FIN) AF: 0.0118 AC: 299 AN: 25319

Middle Eastern (MID) AF: 0.0160 AC: 24 AN: 1504

European-Non Finnish (NFE) AF: 0.0115 AC: 4107 AN: 357868

Other (OTH) AF: 0.0182 AC: 388 AN: 21363

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000934 AC: 60 AN: 64213 Hom.: 4 Cov.: 0 AF XY: 0.000789 AC XY: 9 AN XY: 11401

African (AFR) AF: 0.00259 AC: 33 AN: 12722

American (AMR) AF: 0.000680 AC: 3 AN: 4414

Ashkenazi Jewish (ASJ) AF: 0.000500 AC: 1 AN: 2002

East Asian (EAS) AF: 0.00 AC: 0 AN: 1437

South Asian (SAS) AF: 0.00 AC: 0 AN: 965

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 75

European-Non Finnish (NFE) AF: 0.000579 AC: 23 AN: 39748

Other (OTH) AF: 0.00 AC: 0 AN: 788

Alfa AF: 0.0136 Hom.: 585

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Syndromic X-linked intellectual disability 14 Benign:2

Mar 29, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.065
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs55712755; hg19: chrX-118985711;