X-119837749-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_080632.3(UPF3B):c.1302+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,207,456 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_080632.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.1302+8T>C | splice_region_variant, intron_variant | ENST00000276201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.1302+8T>C | splice_region_variant, intron_variant | 1 | NM_080632.3 | A1 | |||
UPF3B | ENST00000345865.6 | c.1263+8T>C | splice_region_variant, intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111626Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33804
GnomAD3 exomes AF: 0.0000940 AC: 17AN: 180822Hom.: 0 AF XY: 0.000121 AC XY: 8AN XY: 66074
GnomAD4 exome AF: 0.0000301 AC: 33AN: 1095782Hom.: 0 Cov.: 31 AF XY: 0.0000636 AC XY: 23AN XY: 361884
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111674Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33862
ClinVar
Submissions by phenotype
Syndromic X-linked intellectual disability 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 18, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | UPF3B: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at