6-82171555-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015525.4(IBTK):āc.3932T>Cā(p.Ile1311Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000126 in 1,590,824 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_015525.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IBTK | NM_015525.4 | c.3932T>C | p.Ile1311Thr | missense_variant, splice_region_variant | 29/29 | ENST00000306270.12 | |
IBTK | NM_001300906.2 | c.3887T>C | p.Ile1296Thr | missense_variant, splice_region_variant | 29/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IBTK | ENST00000306270.12 | c.3932T>C | p.Ile1311Thr | missense_variant, splice_region_variant | 29/29 | 1 | NM_015525.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1438650Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 713880
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.3932T>C (p.I1311T) alteration is located in exon 29 (coding exon 28) of the IBTK gene. This alteration results from a T to C substitution at nucleotide position 3932, causing the isoleucine (I) at amino acid position 1311 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at