3-44778112-TAGG-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The ENST00000326047.9(KIF15):c.247-1_248del variant causes a splice acceptor, coding sequence change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,164 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely risk allele (no stars).
Frequency
Consequence
ENST00000326047.9 splice_acceptor, coding_sequence
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF15 | NM_020242.3 | c.247-1_248del | splice_acceptor_variant, coding_sequence_variant | 4/35 | ENST00000326047.9 | NP_064627.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF15 | ENST00000326047.9 | c.247-1_248del | splice_acceptor_variant, coding_sequence_variant | 4/35 | 1 | NM_020242.3 | ENSP00000324020 | P1 | ||
KIF15 | ENST00000438321.5 | c.204-1_205del | splice_acceptor_variant, coding_sequence_variant, NMD_transcript_variant | 3/34 | 1 | ENSP00000406939 | ||||
KIF15 | ENST00000481166.6 | c.-83-2771_-83-2769del | intron_variant | 5 | ENSP00000425499 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458914Hom.: 0 AF XY: 0.0000110 AC XY: 8AN XY: 726054
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74392
ClinVar
Submissions by phenotype
Pulmonary fibrosis Pathogenic:1
Likely risk allele, no assertion criteria provided | research | Garcia Pulmonary Genetics Research Laboratory, Columbia University Irving Medical Center | Jun 09, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at