3-44778112-TAGG-T
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_020242.3(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
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
KIF15
NM_020242.3 splice_acceptor, coding_sequence
NM_020242.3 splice_acceptor, coding_sequence
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
KIF15 (HGNC:17273): (kinesin family member 15) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Multiple lines of computational evidence support a deleterious effect 2: max_spliceai, phyloP100way_vertebrate [when was below the threshold]
PP5
Variant 3-44778112-TAGG-T is Pathogenic according to our data. Variant chr3-44778112-TAGG-T is described in ClinVar as [Likely_risk_allele]. Clinvar id is 1695929.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_pathogenic, oryginal submission is: [Likely_risk_allele].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF15 | NM_020242.3 | c.247-1_248del | splice_acceptor_variant, coding_sequence_variant | 4/35 | ENST00000326047.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF15 | ENST00000326047.9 | c.247-1_248del | splice_acceptor_variant, coding_sequence_variant | 4/35 | 1 | NM_020242.3 | P1 | ||
KIF15 | ENST00000438321.5 | c.204-1_205del | splice_acceptor_variant, coding_sequence_variant, NMD_transcript_variant | 3/34 | 1 | ||||
KIF15 | ENST00000481166.6 | c.-83-2771_-83-2769del | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458914Hom.: 0 AF XY: 0.0000110 AC XY: 8AN XY: 726054
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74392
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ClinVar
Significance: Likely risk allele
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
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
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Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at