9-34179039-A-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001171201.1(UBAP1):c.25A>T(p.Arg9Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,263,426 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001171201.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBAP1 | NM_016525.5 | upstream_gene_variant | ENST00000297661.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBAP1 | ENST00000625521.2 | c.25A>T | p.Arg9Trp | missense_variant | 1/6 | 2 | |||
UBAP1 | ENST00000379186.8 | c.-209A>T | 5_prime_UTR_variant | 1/6 | 5 | ||||
UBAP1 | ENST00000297661.9 | upstream_gene_variant | 1 | NM_016525.5 | P1 | ||||
UBAP1 | ENST00000626262.2 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 151986Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000668 AC: 11AN: 16458Hom.: 0 AF XY: 0.000676 AC XY: 5AN XY: 7394
GnomAD4 exome AF: 0.00119 AC: 1327AN: 1111322Hom.: 2 Cov.: 33 AF XY: 0.00115 AC XY: 608AN XY: 530384
GnomAD4 genome AF: 0.000329 AC: 50AN: 152104Hom.: 0 Cov.: 31 AF XY: 0.000269 AC XY: 20AN XY: 74338
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2024 | The c.25A>T (p.R9W) alteration is located in exon 1 (coding exon 1) of the UBAP1 gene. This alteration results from a A to T substitution at nucleotide position 25, causing the arginine (R) at amino acid position 9 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
UBAP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 17, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at