6-82173398-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015525.4(IBTK):āc.3766A>Gā(p.Ile1256Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015525.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IBTK | NM_015525.4 | c.3766A>G | p.Ile1256Val | missense_variant | 27/29 | ENST00000306270.12 | |
IBTK | NM_001300906.2 | c.3721A>G | p.Ile1241Val | missense_variant | 27/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IBTK | ENST00000306270.12 | c.3766A>G | p.Ile1256Val | missense_variant | 27/29 | 1 | NM_015525.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251290Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135806
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461440Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 727038
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152258Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.3766A>G (p.I1256V) alteration is located in exon 27 (coding exon 26) of the IBTK gene. This alteration results from a A to G substitution at nucleotide position 3766, causing the isoleucine (I) at amino acid position 1256 to be replaced by a valine (V). 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