5-140647913-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006083.4(IK):c.5C>T(p.Pro2Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,676 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2R) has been classified as Uncertain significance.
Frequency
Consequence
NM_006083.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IK | NM_006083.4 | c.5C>T | p.Pro2Leu | missense_variant | Exon 1 of 20 | ENST00000417647.7 | NP_006074.2 | |
MIR3655 | NR_037428.1 | n.70C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
TMCO6 | XM_047417354.1 | c.*1096C>T | downstream_gene_variant | XP_047273310.1 | ||||
MIR3655 | unassigned_transcript_869 | n.*49C>T | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249272Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135230
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461676Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727126
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at