Variant X-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_080632.3(UPF3B):c.263+18_263+19insAAAAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 40 hom., 18 hem., cov: 0)

Exomes 𝑓: 0.00049 ( 6 hom. 38 hem. )

Failed GnomAD Quality Control

Consequence

UPF3B
NM_080632.3 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0650

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-119851748-C-CTTTTTTTTTTTTTTTTTTTT is Benign according to our data. Variant chrX-119851748-C-CTTTTTTTTTTTTTTTTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 1669889.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00335 (215/64195) while in subpopulation AFR AF= 0.0159 (202/12704). AF 95% confidence interval is 0.0141. There are 40 homozygotes in gnomad4. There are 18 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 40 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UPF3B	NM_080632.3 linkuse as main transcript	c.263+18_263+19insAAAAAAAAAAAAAAAAAAAA		intron_variant		ENST00000276201.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UPF3B	ENST00000276201.7 linkuse as main transcript	c.263+18_263+19insAAAAAAAAAAAAAAAAAAAA		intron_variant		1	NM_080632.3	A1	Q9BZI7-1
UPF3B	ENST00000345865.6 linkuse as main transcript	c.263+18_263+19insAAAAAAAAAAAAAAAAAAAA		intron_variant		1		P4	Q9BZI7-2

Frequencies

GnomAD3 genomes

AF:

0.00335

AC:

215

AN:

64203

Hom.:

Cov.:

AF XY:

0.00158

AC XY:

AN XY:

11403

show subpopulations

Gnomad AFR

AF:

0.0159

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000680

Gnomad ASJ

AF:

0.000500

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00102

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000151

Gnomad OTH

AF:

0.00257

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000490

AC:

243

AN:

495603

Hom.:

Cov.:

AF XY:

0.000260

AC XY:

AN XY:

145905

show subpopulations

Gnomad4 AFR exome

AF:

0.00644

Gnomad4 AMR exome

AF:

0.00247

Gnomad4 ASJ exome

AF:

0.000613

Gnomad4 EAS exome

AF:

0.00159

Gnomad4 SAS exome

AF:

0.00167

Gnomad4 FIN exome

AF:

0.000190

Gnomad4 NFE exome

AF:

0.000178

Gnomad4 OTH exome

AF:

0.000625

GnomAD4 genome

AF:

0.00335

AC:

215

AN:

64195

Hom.:

Cov.:

AF XY:

0.00158

AC XY:

AN XY:

11401

show subpopulations

Gnomad4 AFR

AF:

0.0159

Gnomad4 AMR

AF:

0.000680

Gnomad4 ASJ

AF:

0.000500

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000151

Gnomad4 OTH

AF:

0.00254

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Syndromic X-linked intellectual disability 14

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 06, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over