chr11-122779487-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032873.5(UBASH3B):c.403-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,613,518 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 24 hom., cov: 32)
Exomes 𝑓: 0.00079 ( 14 hom. )
Consequence
UBASH3B
NM_032873.5 splice_polypyrimidine_tract, intron
NM_032873.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0001657
2
Clinical Significance
Conservation
PhyloP100: -0.157
Genes affected
UBASH3B (HGNC:29884): (ubiquitin associated and SH3 domain containing B) This gene encodes a protein that contains a ubiquitin associated domain at the N-terminus, an SH3 domain, and a C-terminal domain with similarities to the catalytic motif of phosphoglycerate mutase. The encoded protein was found to inhibit endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 11-122779487-T-C is Benign according to our data. Variant chr11-122779487-T-C is described in ClinVar as [Benign]. Clinvar id is 781237.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00838 (1276/152332) while in subpopulation AFR AF= 0.0294 (1222/41564). AF 95% confidence interval is 0.028. There are 24 homozygotes in gnomad4. There are 596 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1278 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBASH3B | NM_032873.5 | c.403-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000284273.6 | |||
UBASH3B | NM_001363365.2 | c.298-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
UBASH3B | XM_005271712.4 | c.487-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
UBASH3B | XM_011543041.3 | c.346-10T>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBASH3B | ENST00000284273.6 | c.403-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032873.5 | P1 | |||
ENST00000649590.1 | n.74-13438A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00840 AC: 1278AN: 152214Hom.: 24 Cov.: 32
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GnomAD3 exomes AF: 0.00228 AC: 570AN: 249636Hom.: 12 AF XY: 0.00169 AC XY: 228AN XY: 135072
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GnomAD4 exome AF: 0.000787 AC: 1150AN: 1461186Hom.: 14 Cov.: 33 AF XY: 0.000677 AC XY: 492AN XY: 726916
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at