rs201188361
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_014714.4(IFT140):c.634G>C(p.Gly212Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar.
Frequency
Consequence
NM_014714.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.634G>C | p.Gly212Arg | missense_variant, splice_region_variant | 6/31 | ENST00000426508.7 | |
LOC105371046 | NR_135176.1 | n.59+11591C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.634G>C | p.Gly212Arg | missense_variant, splice_region_variant | 6/31 | 5 | NM_014714.4 | P1 | |
ENST00000563162.1 | n.59+11591C>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
IFT140 | ENST00000439987.6 | n.695G>C | splice_region_variant, non_coding_transcript_exon_variant | 5/19 | 2 | ||||
IFT140 | ENST00000397417.6 | c.329-7756G>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251364Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135870
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at