rs200584307
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005886.3(KATNB1):c.856-5T>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00657 in 1,598,136 control chromosomes in the GnomAD database, including 48 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 Likely benign (★★).
Frequency
Consequence
NM_005886.3 splice_region, splice_polypyrimidine_tract, 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 |
---|---|---|---|---|---|---|---|
KATNB1 | NM_005886.3 | c.856-5T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379661.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KATNB1 | ENST00000379661.8 | c.856-5T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_005886.3 | P1 | |||
KATNB1 | ENST00000566611.5 | n.2168T>G | non_coding_transcript_exon_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00484 AC: 736AN: 152174Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00486 AC: 1173AN: 241452Hom.: 7 AF XY: 0.00494 AC XY: 649AN XY: 131388
GnomAD4 exome AF: 0.00675 AC: 9756AN: 1445844Hom.: 43 Cov.: 36 AF XY: 0.00658 AC XY: 4721AN XY: 717664
GnomAD4 genome ? AF: 0.00483 AC: 736AN: 152292Hom.: 5 Cov.: 33 AF XY: 0.00423 AC XY: 315AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | KATNB1: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 01, 2016 | - - |
KATNB1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 30, 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