1-206476673-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014002.4(IKBKE):c.541-5G>A 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 0.0000223 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014002.4 splice_region, splice_polypyrimidine_tract, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IKBKE | NM_014002.4 | c.541-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000581977.7 | NP_054721.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IKBKE | ENST00000581977.7 | c.541-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014002.4 | ENSP00000464030 | P1 | |||
IKBKE | ENST00000578328.6 | c.541-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000473833 | |||||
IKBKE | ENST00000584998.5 | c.286-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000462396 | |||||
IKBKE | ENST00000605818.5 | n.886-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250358Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135428
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461780Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727202
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74478
ClinVar
Submissions by phenotype
Autoimmune connective tissue disease and vasculitis Uncertain:1
Uncertain significance, flagged submission | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Oct 04, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Dec 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at