chr2-209777564-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001371986.1(UNC80):c.600+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,598,946 control chromosomes in the GnomAD database, including 28 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_001371986.1 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC80 | NM_001371986.1 | c.600+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000673920.1 | |||
UNC80 | NM_032504.2 | c.600+5G>A | splice_donor_5th_base_variant, intron_variant | ||||
UNC80 | NM_182587.4 | c.600+5G>A | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC80 | ENST00000673920.1 | c.600+5G>A | splice_donor_5th_base_variant, intron_variant | NM_001371986.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00741 AC: 1128AN: 152216Hom.: 20 Cov.: 33
GnomAD3 exomes AF: 0.00205 AC: 484AN: 236034Hom.: 8 AF XY: 0.00165 AC XY: 209AN XY: 126942
GnomAD4 exome AF: 0.000760 AC: 1100AN: 1446612Hom.: 8 Cov.: 31 AF XY: 0.000673 AC XY: 483AN XY: 717966
GnomAD4 genome ? AF: 0.00740 AC: 1127AN: 152334Hom.: 20 Cov.: 33 AF XY: 0.00780 AC XY: 581AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 24, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
UNC80-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 21, 2019 | This variant is classified as 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